Starting phenix.real_space_refine on Sat Feb 17 04:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd3_27333/02_2024/8dd3_27333_updated.pdb" } resolution = 2.9 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= 0.003 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 97 5.16 5 C 11276 2.51 5 N 2835 2.21 5 O 3251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17459 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" 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: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R63': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R63': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'R63': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.42, per 1000 atoms: 0.54 Number of scatterers: 17459 At special positions: 0 Unit cell: (159.692, 134.875, 120.848, 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 97 16.00 O 3251 8.00 N 2835 7.00 C 11276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 28 sheets defined 30.3% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 218 through 241 removed outlier: 4.401A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.141A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 Processing helix chain 'A' and resid 280 through 308 removed outlier: 4.123A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 338 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.584A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.785A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.563A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 346 Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.553A pdb=" N ILE C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 4.008A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 246 removed outlier: 4.624A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.138A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.759A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.135A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 256 removed outlier: 4.742A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.687A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 285 removed outlier: 3.669A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 323 removed outlier: 4.166A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.172A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.585A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 209 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= D, first strand: chain 'A' and resid 147 through 150 Processing sheet with id= E, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.425A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= G, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.240A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 104 through 109 removed outlier: 6.898A pdb=" N ARG B 136 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B 107 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 134 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.400A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.596A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.797A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.369A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.372A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 51 through 55 Processing sheet with id= P, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.913A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.683A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.983A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.167A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.254A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.594A pdb=" N THR J 115 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP J 57 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Y, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.017A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.590A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.514A pdb=" N VAL K 12 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP K 47 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 97 through 99 removed outlier: 4.232A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2247 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: 6.13 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2671 1.31 - 1.43: 5285 1.43 - 1.56: 9774 1.56 - 1.69: 2 1.69 - 1.82: 167 Bond restraints: 17899 Sorted by residual: bond pdb=" C16 R63 D 701 " pdb=" O18 R63 D 701 " ideal model delta sigma weight residual 1.398 1.320 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C16 R63 C 403 " pdb=" O18 R63 C 403 " ideal model delta sigma weight residual 1.398 1.325 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C04 R63 A 403 " pdb=" C05 R63 A 403 " ideal model delta sigma weight residual 1.389 1.461 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C04 R63 C 403 " pdb=" C05 R63 C 403 " ideal model delta sigma weight residual 1.389 1.460 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C16 R63 A 403 " pdb=" O18 R63 A 403 " ideal model delta sigma weight residual 1.398 1.329 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 17894 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.94: 347 105.94 - 113.51: 10121 113.51 - 121.07: 8909 121.07 - 128.63: 4817 128.63 - 136.20: 152 Bond angle restraints: 24346 Sorted by residual: angle pdb=" C03 R63 A 403 " pdb=" C15 R63 A 403 " pdb=" C16 R63 A 403 " ideal model delta sigma weight residual 152.20 121.29 30.91 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C16 R63 A 403 " pdb=" C15 R63 A 403 " pdb=" N14 R63 A 403 " ideal model delta sigma weight residual 86.39 116.94 -30.55 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C03 R63 D 701 " pdb=" C15 R63 D 701 " pdb=" C16 R63 D 701 " ideal model delta sigma weight residual 152.20 124.70 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" C16 R63 D 701 " pdb=" C15 R63 D 701 " pdb=" N14 R63 D 701 " ideal model delta sigma weight residual 86.39 113.43 -27.04 3.00e+00 1.11e-01 8.12e+01 angle pdb=" C03 R63 C 403 " pdb=" C15 R63 C 403 " pdb=" C16 R63 C 403 " ideal model delta sigma weight residual 152.20 126.09 26.11 3.00e+00 1.11e-01 7.57e+01 ... (remaining 24341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 10167 21.47 - 42.94: 547 42.94 - 64.40: 40 64.40 - 85.87: 45 85.87 - 107.34: 18 Dihedral angle restraints: 10817 sinusoidal: 4561 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual 93.00 48.01 44.99 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 10814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 2795 0.190 - 0.380: 8 0.380 - 0.570: 1 0.570 - 0.760: 2 0.760 - 0.950: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.45 0.95 2.00e-02 2.50e+03 2.25e+03 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 111 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.07 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 2804 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " -0.184 2.00e-02 2.50e+03 3.86e-01 1.86e+03 pdb=" CG ASN C 80 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " 0.677 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.469 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " -0.070 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" CG ASN A 149 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " 0.116 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 111 " 0.031 2.00e-02 2.50e+03 7.31e-02 6.68e+01 pdb=" CG ASN B 111 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 111 " -0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN B 111 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.086 2.00e-02 2.50e+03 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 186 2.60 - 3.17: 15176 3.17 - 3.75: 25651 3.75 - 4.32: 37990 4.32 - 4.90: 63471 Nonbonded interactions: 142474 Sorted by model distance: nonbonded pdb=" O GLY I 30 " pdb=" OG1 THR I 31 " model vdw 2.021 2.440 nonbonded pdb=" OD1 ASP D 63 " pdb=" OG1 THR D 134 " model vdw 2.026 2.440 nonbonded pdb=" OG SER C 308 " pdb=" OE1 GLN C 309 " model vdw 2.052 2.440 nonbonded pdb=" OG SER E 217 " pdb=" OH TYR E 220 " model vdw 2.099 2.440 nonbonded pdb=" OG SER C 247 " pdb=" OH TYR C 299 " model vdw 2.099 2.440 ... (remaining 142469 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.010 Extract box with map and model: 5.980 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 50.780 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.005 0.078 17899 Z= 0.352 Angle : 0.819 30.908 24346 Z= 0.362 Chirality : 0.052 0.950 2807 Planarity : 0.004 0.071 2988 Dihedral : 14.338 107.341 6770 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.77 (0.19), residues: 2103 helix: 2.72 (0.20), residues: 572 sheet: -0.30 (0.20), residues: 679 loop : -0.24 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 256 HIS 0.005 0.001 HIS C 267 PHE 0.022 0.002 PHE D 226 TYR 0.015 0.001 TYR E 350 ARG 0.008 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PRO cc_start: 0.6476 (Cg_exo) cc_final: 0.6047 (Cg_endo) REVERT: C 48 ASP cc_start: 0.7634 (m-30) cc_final: 0.7416 (m-30) REVERT: C 185 GLN cc_start: 0.7830 (pt0) cc_final: 0.7306 (pt0) REVERT: D 190 GLN cc_start: 0.8205 (pt0) cc_final: 0.7829 (pt0) REVERT: E 336 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6889 (mtt180) REVERT: E 340 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: E 351 TRP cc_start: 0.7180 (m100) cc_final: 0.6926 (m100) REVERT: I 13 MET cc_start: 0.6153 (pmm) cc_final: 0.5881 (pmm) REVERT: I 17 GLU cc_start: 0.7073 (tt0) cc_final: 0.6837 (tt0) REVERT: J 34 MET cc_start: 0.8828 (mmp) cc_final: 0.8401 (mpp) REVERT: J 73 ASP cc_start: 0.7828 (t0) cc_final: 0.7465 (t0) REVERT: L 24 LYS cc_start: 0.8264 (tttp) cc_final: 0.7980 (mtpp) REVERT: K 63 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8650 (mmtm) REVERT: K 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7761 (t0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 1.3099 time to fit residues: 488.2252 Evaluate side-chains 269 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN C 113 ASN C 119 HIS D 229 GLN E 163 HIS E 347 ASN K 55 ASN K 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17899 Z= 0.236 Angle : 0.609 8.744 24346 Z= 0.309 Chirality : 0.046 0.854 2807 Planarity : 0.004 0.053 2988 Dihedral : 9.190 84.271 2830 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.02 % Allowed : 9.19 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.17 (0.19), residues: 2103 helix: 3.11 (0.20), residues: 572 sheet: 0.05 (0.20), residues: 677 loop : -0.16 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 319 HIS 0.004 0.001 HIS E 163 PHE 0.016 0.002 PHE B 304 TYR 0.022 0.001 TYR I 49 ARG 0.005 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 285 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8444 (pt) cc_final: 0.8175 (mt) REVERT: B 90 MET cc_start: 0.8493 (tpt) cc_final: 0.8260 (tpt) REVERT: B 131 MET cc_start: 0.8987 (ptm) cc_final: 0.8751 (ptm) REVERT: B 266 MET cc_start: 0.8028 (tpt) cc_final: 0.7680 (tpt) REVERT: B 277 LEU cc_start: 0.6764 (pt) cc_final: 0.6563 (pp) REVERT: C 48 ASP cc_start: 0.7559 (m-30) cc_final: 0.7334 (m-30) REVERT: C 185 GLN cc_start: 0.7830 (pt0) cc_final: 0.7175 (pt0) REVERT: D 190 GLN cc_start: 0.8214 (pt0) cc_final: 0.7827 (pt0) REVERT: D 242 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.6548 (mp-120) REVERT: J 34 MET cc_start: 0.8816 (mmp) cc_final: 0.8279 (mpp) REVERT: J 52 ASP cc_start: 0.8230 (t0) cc_final: 0.7978 (t0) REVERT: L 24 LYS cc_start: 0.8333 (tttp) cc_final: 0.8026 (mtpp) REVERT: L 83 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8233 (pp) REVERT: K 63 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8628 (mmtm) REVERT: K 73 ASP cc_start: 0.7983 (t0) cc_final: 0.7770 (t0) outliers start: 38 outliers final: 19 residues processed: 304 average time/residue: 1.3565 time to fit residues: 460.0801 Evaluate side-chains 288 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 229 GLN E 318 HIS K 55 ASN K 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17899 Z= 0.257 Angle : 0.583 10.058 24346 Z= 0.295 Chirality : 0.045 0.597 2807 Planarity : 0.004 0.050 2988 Dihedral : 7.556 79.519 2830 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.34 % Allowed : 12.32 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.19), residues: 2103 helix: 3.01 (0.20), residues: 574 sheet: 0.15 (0.20), residues: 680 loop : -0.15 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 319 HIS 0.006 0.001 HIS E 163 PHE 0.016 0.002 PHE A 306 TYR 0.016 0.001 TYR C 299 ARG 0.004 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8440 (pt) cc_final: 0.8181 (mt) REVERT: B 131 MET cc_start: 0.8954 (ptm) cc_final: 0.8728 (ptm) REVERT: B 277 LEU cc_start: 0.6969 (pt) cc_final: 0.6708 (pp) REVERT: C 48 ASP cc_start: 0.7520 (m-30) cc_final: 0.7307 (m-30) REVERT: C 81 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (pp) REVERT: C 185 GLN cc_start: 0.7798 (pt0) cc_final: 0.7136 (pt0) REVERT: D 190 GLN cc_start: 0.8200 (pt0) cc_final: 0.7807 (pt0) REVERT: D 242 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6235 (mp-120) REVERT: D 243 VAL cc_start: 0.8661 (p) cc_final: 0.8351 (t) REVERT: E 332 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: J 34 MET cc_start: 0.8832 (mmp) cc_final: 0.8296 (mpp) REVERT: L 24 LYS cc_start: 0.8342 (tttp) cc_final: 0.8106 (mtpp) REVERT: L 83 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8179 (pp) REVERT: K 63 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8636 (mmtm) REVERT: K 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7823 (t0) outliers start: 44 outliers final: 32 residues processed: 296 average time/residue: 1.3108 time to fit residues: 433.6772 Evaluate side-chains 292 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN L 79 GLN K 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17899 Z= 0.265 Angle : 0.581 10.367 24346 Z= 0.294 Chirality : 0.044 0.559 2807 Planarity : 0.004 0.050 2988 Dihedral : 6.955 80.866 2830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 13.44 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.21 (0.19), residues: 2103 helix: 2.95 (0.20), residues: 574 sheet: 0.25 (0.20), residues: 681 loop : -0.18 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 319 HIS 0.003 0.001 HIS D 110 PHE 0.018 0.001 PHE D 226 TYR 0.026 0.001 TYR I 49 ARG 0.003 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 272 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.8930 (ptm) cc_final: 0.8703 (ptm) REVERT: C 40 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8284 (mtm) REVERT: C 48 ASP cc_start: 0.7497 (m-30) cc_final: 0.7279 (m-30) REVERT: C 81 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (pp) REVERT: C 185 GLN cc_start: 0.7799 (pt0) cc_final: 0.7187 (pt0) REVERT: D 190 GLN cc_start: 0.8167 (pt0) cc_final: 0.7793 (pt0) REVERT: D 242 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6137 (mp-120) REVERT: D 243 VAL cc_start: 0.8666 (p) cc_final: 0.8316 (t) REVERT: E 296 MET cc_start: 0.6371 (ppp) cc_final: 0.6123 (pp-130) REVERT: E 308 PHE cc_start: 0.7904 (t80) cc_final: 0.7695 (t80) REVERT: E 332 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: J 34 MET cc_start: 0.8858 (mmp) cc_final: 0.8316 (mpp) REVERT: L 13 MET cc_start: 0.6844 (pp-130) cc_final: 0.6637 (ppp) REVERT: L 24 LYS cc_start: 0.8356 (tttp) cc_final: 0.8132 (mtpp) REVERT: L 83 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8202 (pp) REVERT: K 63 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8639 (mmtm) REVERT: K 73 ASP cc_start: 0.8028 (t0) cc_final: 0.7819 (t0) outliers start: 61 outliers final: 38 residues processed: 299 average time/residue: 1.3274 time to fit residues: 443.1634 Evaluate side-chains 299 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 148 optimal weight: 0.0000 chunk 82 optimal weight: 0.0870 chunk 170 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN K 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17899 Z= 0.143 Angle : 0.540 10.546 24346 Z= 0.270 Chirality : 0.042 0.444 2807 Planarity : 0.003 0.045 2988 Dihedral : 6.279 82.414 2830 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.39 % Allowed : 14.98 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.33 (0.19), residues: 2103 helix: 2.99 (0.20), residues: 574 sheet: 0.26 (0.20), residues: 698 loop : 0.01 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 319 HIS 0.003 0.000 HIS E 163 PHE 0.017 0.001 PHE C 330 TYR 0.014 0.001 TYR E 319 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.8457 (tpt) cc_final: 0.8143 (tpt) REVERT: B 131 MET cc_start: 0.8889 (ptm) cc_final: 0.8595 (ptm) REVERT: B 213 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8264 (mmp) REVERT: B 277 LEU cc_start: 0.6918 (pt) cc_final: 0.6679 (pp) REVERT: C 40 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (mtm) REVERT: C 81 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8834 (pp) REVERT: C 185 GLN cc_start: 0.7816 (pt0) cc_final: 0.7189 (pt0) REVERT: D 190 GLN cc_start: 0.8159 (pt0) cc_final: 0.7756 (pt0) REVERT: D 242 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: D 294 TYR cc_start: 0.8136 (t80) cc_final: 0.7799 (t80) REVERT: E 296 MET cc_start: 0.6309 (ppp) cc_final: 0.6094 (pp-130) REVERT: E 332 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: J 34 MET cc_start: 0.8815 (mmp) cc_final: 0.8211 (mpp) REVERT: J 52 ASP cc_start: 0.8064 (t0) cc_final: 0.7774 (t0) REVERT: L 24 LYS cc_start: 0.8333 (tttp) cc_final: 0.8110 (mtpp) REVERT: K 63 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8672 (mmtm) REVERT: K 73 ASP cc_start: 0.8092 (t0) cc_final: 0.7856 (t0) outliers start: 45 outliers final: 20 residues processed: 295 average time/residue: 1.3224 time to fit residues: 436.6584 Evaluate side-chains 284 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 0.0270 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN B 242 GLN D 229 GLN E 347 ASN K 55 ASN K 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17899 Z= 0.162 Angle : 0.540 11.173 24346 Z= 0.268 Chirality : 0.042 0.416 2807 Planarity : 0.003 0.045 2988 Dihedral : 6.060 83.036 2830 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.66 % Allowed : 15.83 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.33 (0.19), residues: 2103 helix: 2.94 (0.21), residues: 576 sheet: 0.31 (0.19), residues: 704 loop : -0.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 PHE 0.017 0.001 PHE C 330 TYR 0.026 0.001 TYR I 49 ARG 0.003 0.000 ARG E 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8414 (pp) REVERT: B 131 MET cc_start: 0.8904 (ptm) cc_final: 0.8653 (ptm) REVERT: B 277 LEU cc_start: 0.6959 (pt) cc_final: 0.6704 (pp) REVERT: C 40 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: C 81 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 185 GLN cc_start: 0.7776 (pt0) cc_final: 0.7145 (pt0) REVERT: D 190 GLN cc_start: 0.8161 (pt0) cc_final: 0.7754 (pt0) REVERT: D 242 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: D 243 VAL cc_start: 0.8520 (p) cc_final: 0.8206 (t) REVERT: D 294 TYR cc_start: 0.8095 (t80) cc_final: 0.7703 (t80) REVERT: E 296 MET cc_start: 0.6310 (ppp) cc_final: 0.6086 (pp-130) REVERT: E 351 TRP cc_start: 0.7076 (m100) cc_final: 0.6730 (m100) REVERT: J 52 ASP cc_start: 0.8066 (t0) cc_final: 0.7791 (t0) REVERT: L 24 LYS cc_start: 0.8391 (tttp) cc_final: 0.8158 (mtpp) REVERT: K 63 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8615 (mmtm) outliers start: 50 outliers final: 26 residues processed: 295 average time/residue: 1.3088 time to fit residues: 435.3753 Evaluate side-chains 292 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 229 GLN D 248 ASN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17899 Z= 0.163 Angle : 0.543 11.658 24346 Z= 0.270 Chirality : 0.042 0.395 2807 Planarity : 0.003 0.044 2988 Dihedral : 5.930 83.670 2830 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.44 % Allowed : 16.62 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2103 helix: 2.92 (0.21), residues: 576 sheet: 0.34 (0.19), residues: 704 loop : 0.02 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 319 HIS 0.002 0.001 HIS B 110 PHE 0.020 0.001 PHE E 308 TYR 0.026 0.001 TYR E 334 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 273 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 131 MET cc_start: 0.8900 (ptm) cc_final: 0.8660 (ptm) REVERT: B 277 LEU cc_start: 0.6946 (pt) cc_final: 0.6696 (pp) REVERT: C 40 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8177 (mtm) REVERT: C 81 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8728 (pp) REVERT: C 185 GLN cc_start: 0.7773 (pt0) cc_final: 0.7141 (pt0) REVERT: D 190 GLN cc_start: 0.8152 (pt0) cc_final: 0.7751 (pt0) REVERT: D 242 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: D 243 VAL cc_start: 0.8456 (p) cc_final: 0.8130 (t) REVERT: D 294 TYR cc_start: 0.8143 (t80) cc_final: 0.7741 (t80) REVERT: E 331 MET cc_start: 0.4714 (mmm) cc_final: 0.4481 (mmm) REVERT: E 332 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: E 351 TRP cc_start: 0.7065 (m100) cc_final: 0.6764 (m100) REVERT: J 34 MET cc_start: 0.8767 (tpp) cc_final: 0.7965 (mpp) REVERT: J 52 ASP cc_start: 0.8094 (t0) cc_final: 0.7887 (t0) REVERT: L 13 MET cc_start: 0.7015 (pp-130) cc_final: 0.6655 (ppp) REVERT: L 24 LYS cc_start: 0.8410 (tttp) cc_final: 0.8164 (mtpp) REVERT: K 63 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8603 (mmtm) outliers start: 46 outliers final: 30 residues processed: 297 average time/residue: 1.2991 time to fit residues: 432.2535 Evaluate side-chains 298 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 229 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17899 Z= 0.261 Angle : 0.592 12.100 24346 Z= 0.297 Chirality : 0.044 0.408 2807 Planarity : 0.004 0.046 2988 Dihedral : 6.092 84.054 2830 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.76 % Allowed : 17.15 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.28 (0.19), residues: 2103 helix: 2.87 (0.21), residues: 574 sheet: 0.33 (0.19), residues: 684 loop : -0.05 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 319 HIS 0.004 0.001 HIS B 110 PHE 0.021 0.002 PHE D 226 TYR 0.026 0.001 TYR I 49 ARG 0.006 0.000 ARG J 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 265 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.8900 (ptm) cc_final: 0.8608 (ptm) REVERT: C 40 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: C 81 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8848 (pp) REVERT: C 185 GLN cc_start: 0.7788 (pt0) cc_final: 0.7154 (pt0) REVERT: C 298 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8535 (tm-30) REVERT: D 190 GLN cc_start: 0.8145 (pt0) cc_final: 0.7757 (pt0) REVERT: D 242 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: D 243 VAL cc_start: 0.8610 (p) cc_final: 0.8199 (t) REVERT: E 317 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7243 (tp) REVERT: E 331 MET cc_start: 0.4849 (mmm) cc_final: 0.4486 (mmm) REVERT: E 332 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: E 351 TRP cc_start: 0.7081 (m100) cc_final: 0.6801 (m100) REVERT: J 52 ASP cc_start: 0.8152 (t0) cc_final: 0.7952 (t0) REVERT: L 24 LYS cc_start: 0.8434 (tttp) cc_final: 0.8190 (mtpp) REVERT: K 63 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8556 (mmtm) outliers start: 52 outliers final: 34 residues processed: 292 average time/residue: 1.2968 time to fit residues: 424.0897 Evaluate side-chains 302 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 263 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17899 Z= 0.257 Angle : 0.600 12.406 24346 Z= 0.300 Chirality : 0.044 0.409 2807 Planarity : 0.004 0.046 2988 Dihedral : 6.127 84.850 2830 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 17.74 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.25 (0.19), residues: 2103 helix: 2.87 (0.21), residues: 572 sheet: 0.31 (0.19), residues: 684 loop : -0.08 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 319 HIS 0.004 0.001 HIS A 267 PHE 0.023 0.001 PHE C 330 TYR 0.027 0.001 TYR I 49 ARG 0.004 0.000 ARG J 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 265 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.8916 (ptm) cc_final: 0.8638 (ptm) REVERT: B 277 LEU cc_start: 0.7014 (pt) cc_final: 0.6726 (pp) REVERT: C 40 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8242 (mtm) REVERT: C 81 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (pp) REVERT: C 185 GLN cc_start: 0.7828 (pt0) cc_final: 0.7201 (pt0) REVERT: D 190 GLN cc_start: 0.8138 (pt0) cc_final: 0.7756 (pt0) REVERT: D 242 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: D 243 VAL cc_start: 0.8584 (p) cc_final: 0.8169 (t) REVERT: D 294 TYR cc_start: 0.8290 (t80) cc_final: 0.8030 (t80) REVERT: E 331 MET cc_start: 0.4862 (mmm) cc_final: 0.4564 (mmm) REVERT: E 332 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: E 351 TRP cc_start: 0.7090 (m100) cc_final: 0.6805 (m100) REVERT: J 52 ASP cc_start: 0.8197 (t0) cc_final: 0.7996 (t0) REVERT: K 63 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8548 (mmtm) outliers start: 52 outliers final: 34 residues processed: 292 average time/residue: 1.2873 time to fit residues: 421.5164 Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 0.0040 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 130 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 242 GLN C 243 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17899 Z= 0.170 Angle : 0.582 12.637 24346 Z= 0.288 Chirality : 0.042 0.375 2807 Planarity : 0.003 0.045 2988 Dihedral : 5.973 86.115 2830 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.18 % Allowed : 18.43 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.31 (0.19), residues: 2103 helix: 2.91 (0.21), residues: 573 sheet: 0.29 (0.19), residues: 709 loop : 0.01 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 319 HIS 0.002 0.001 HIS A 267 PHE 0.023 0.001 PHE C 330 TYR 0.028 0.001 TYR I 49 ARG 0.004 0.000 ARG J 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.8894 (ptm) cc_final: 0.8598 (ptm) REVERT: B 277 LEU cc_start: 0.7076 (pt) cc_final: 0.6799 (pp) REVERT: C 40 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: C 81 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8723 (pp) REVERT: C 185 GLN cc_start: 0.7804 (pt0) cc_final: 0.7173 (pt0) REVERT: C 259 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7492 (mm) REVERT: D 190 GLN cc_start: 0.8149 (pt0) cc_final: 0.7745 (pt0) REVERT: D 242 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: D 294 TYR cc_start: 0.8223 (t80) cc_final: 0.7921 (t80) REVERT: E 331 MET cc_start: 0.4994 (mmm) cc_final: 0.4605 (mmm) REVERT: E 332 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: E 351 TRP cc_start: 0.7056 (m100) cc_final: 0.6768 (m100) REVERT: I 49 TYR cc_start: 0.8578 (p90) cc_final: 0.7659 (p90) outliers start: 41 outliers final: 33 residues processed: 285 average time/residue: 1.2833 time to fit residues: 409.0867 Evaluate side-chains 297 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.0370 chunk 68 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 242 GLN ** L 79 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 = 0.3517 r_free = 0.3517 target = 0.107697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073920 restraints weight = 29992.210| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.38 r_work: 0.2830 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17899 Z= 0.213 Angle : 0.613 18.551 24346 Z= 0.310 Chirality : 0.043 0.370 2807 Planarity : 0.004 0.060 2988 Dihedral : 5.967 86.010 2830 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.60 % Allowed : 18.16 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.19), residues: 2103 helix: 2.84 (0.21), residues: 573 sheet: 0.29 (0.19), residues: 709 loop : -0.02 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 PHE 0.041 0.001 PHE C 323 TYR 0.029 0.001 TYR I 49 ARG 0.004 0.000 ARG J 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7146.31 seconds wall clock time: 127 minutes 29.33 seconds (7649.33 seconds total)