Starting phenix.real_space_refine on Sun Mar 17 03:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql6_14065/03_2024/7ql6_14065_updated.pdb" } resolution = 3.23 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= 0.002 sd= 0.043 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 83 5.16 5 C 10837 2.51 5 N 2603 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16617 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3125 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3466 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2993 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 1 Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3280 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.10, per 1000 atoms: 0.55 Number of scatterers: 16617 At special positions: 0 Unit cell: (100.76, 104.195, 179.765, 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 83 16.00 O 3094 8.00 N 2603 7.00 C 10837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 7.79 Conformation dependent library (CDL) restraints added in 2.7 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 22 sheets defined 37.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.568A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 4.558A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 242 through 261 Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 381 through 430 removed outlier: 4.283A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.522A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.391A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.929A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 305 Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 401 through 459 Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 226 through 248 removed outlier: 4.556A pdb=" N THR C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.667A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.948A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 417 through 477 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 234 removed outlier: 4.447A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.178A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 318 removed outlier: 4.080A pdb=" N ILE D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 420 removed outlier: 4.165A pdb=" N HIS D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.812A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 272 removed outlier: 3.599A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 329 through 333 Processing helix chain 'E' and resid 420 through 469 removed outlier: 3.561A pdb=" N SER E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.952A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.848A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.491A pdb=" N VAL B 29 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN B 159 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 31 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 30 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 80 Processing sheet with id= H, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= I, first strand: chain 'B' and resid 186 through 190 removed outlier: 6.904A pdb=" N ILE B 212 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.666A pdb=" N VAL C 31 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASP C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= L, first strand: chain 'C' and resid 79 through 82 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.015A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 164 through 167 Processing sheet with id= O, first strand: chain 'C' and resid 190 through 194 removed outlier: 6.917A pdb=" N ILE C 220 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 158 through 160 removed outlier: 6.214A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'D' and resid 139 through 147 removed outlier: 3.785A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.795A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= U, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.096A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.967A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2193 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: 5.38 Time building geometry restraints manager: 8.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2598 1.32 - 1.46: 5259 1.46 - 1.59: 9060 1.59 - 1.73: 0 1.73 - 1.86: 135 Bond restraints: 17052 Sorted by residual: bond pdb=" C5 CCE A 601 " pdb=" N6 CCE A 601 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C5 CCE D 601 " pdb=" N6 CCE D 601 " ideal model delta sigma weight residual 1.340 1.452 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" CA ALA D 96 " pdb=" CB ALA D 96 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.67e-02 3.59e+03 1.21e+01 bond pdb=" C PRO E 479 " pdb=" O PRO E 479 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 17047 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.60: 621 106.60 - 113.48: 9776 113.48 - 120.36: 6018 120.36 - 127.23: 6624 127.23 - 134.11: 235 Bond angle restraints: 23274 Sorted by residual: angle pdb=" N PRO E 481 " pdb=" CA PRO E 481 " pdb=" C PRO E 481 " ideal model delta sigma weight residual 113.47 120.62 -7.15 1.43e+00 4.89e-01 2.50e+01 angle pdb=" N PHE B 468 " pdb=" CA PHE B 468 " pdb=" C PHE B 468 " ideal model delta sigma weight residual 113.56 107.05 6.51 1.39e+00 5.18e-01 2.20e+01 angle pdb=" C PRO B 467 " pdb=" CA PRO B 467 " pdb=" CB PRO B 467 " ideal model delta sigma weight residual 111.85 106.17 5.68 1.42e+00 4.96e-01 1.60e+01 angle pdb=" N ALA D 96 " pdb=" CA ALA D 96 " pdb=" C ALA D 96 " ideal model delta sigma weight residual 114.04 109.33 4.71 1.24e+00 6.50e-01 1.44e+01 angle pdb=" N TYR B 134 " pdb=" CA TYR B 134 " pdb=" CB TYR B 134 " ideal model delta sigma weight residual 114.10 110.32 3.78 1.00e+00 1.00e+00 1.43e+01 ... (remaining 23269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 10055 22.56 - 45.12: 355 45.12 - 67.68: 53 67.68 - 90.23: 56 90.23 - 112.79: 39 Dihedral angle restraints: 10558 sinusoidal: 4656 harmonic: 5902 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PHE B 137 " pdb=" C PHE B 137 " pdb=" N ASP B 138 " pdb=" CA ASP B 138 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 10555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2417 0.064 - 0.127: 353 0.127 - 0.191: 21 0.191 - 0.255: 6 0.255 - 0.318: 9 Chirality restraints: 2806 Sorted by residual: chirality pdb=" CA VAL C 31 " pdb=" N VAL C 31 " pdb=" C VAL C 31 " pdb=" CB VAL C 31 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2803 not shown) Planarity restraints: 2837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 92 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C LEU D 92 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 92 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR D 93 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 121 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 122 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 215 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C VAL D 215 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL D 215 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 2834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3669 2.79 - 3.31: 16129 3.31 - 3.84: 28061 3.84 - 4.37: 33163 4.37 - 4.90: 57163 Nonbonded interactions: 138185 Sorted by model distance: nonbonded pdb=" O SER A 226 " pdb=" OG1 THR A 229 " model vdw 2.258 2.440 nonbonded pdb=" O SER D 226 " pdb=" OG1 THR D 229 " model vdw 2.263 2.440 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR B 220 " pdb=" OE2 GLU C 280 " model vdw 2.276 2.440 nonbonded pdb=" O GLY E 182 " pdb=" NZ LYS E 218 " model vdw 2.294 2.520 ... (remaining 138180 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' and (resid 1 through 322 or resid 378 through 421 or resid 601)) selection = (chain 'D' and (resid 1 through 322 or resid 378 through 421 or resid 601)) } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 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: 0.780 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: 4.520 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 47.080 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.004 0.113 17052 Z= 0.293 Angle : 0.671 11.218 23274 Z= 0.335 Chirality : 0.048 0.318 2806 Planarity : 0.004 0.043 2829 Dihedral : 15.259 112.793 6697 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.60 % Allowed : 4.41 % Favored : 94.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1970 helix: 2.24 (0.19), residues: 756 sheet: -0.42 (0.26), residues: 383 loop : -0.83 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.003 0.001 HIS D 385 PHE 0.015 0.001 PHE A 284 TYR 0.012 0.001 TYR D 93 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 360 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8486 (m-40) cc_final: 0.8016 (m110) REVERT: A 238 ASP cc_start: 0.7441 (t0) cc_final: 0.7205 (t0) REVERT: A 252 SER cc_start: 0.9239 (m) cc_final: 0.9016 (p) REVERT: B 250 SER cc_start: 0.8933 (t) cc_final: 0.8694 (m) REVERT: B 442 VAL cc_start: 0.8220 (t) cc_final: 0.7923 (p) REVERT: C 296 MET cc_start: 0.7766 (mtp) cc_final: 0.7482 (mtp) REVERT: C 473 PHE cc_start: 0.7717 (m-10) cc_final: 0.6986 (t80) REVERT: D 144 MET cc_start: 0.6649 (mtt) cc_final: 0.6332 (mtp) REVERT: D 277 TYR cc_start: 0.7499 (m-10) cc_final: 0.6252 (t80) REVERT: D 309 PRO cc_start: 0.8181 (Cg_exo) cc_final: 0.7401 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8580 (mm) cc_final: 0.8258 (mm) REVERT: E 239 LEU cc_start: 0.8737 (tp) cc_final: 0.8484 (tp) REVERT: E 269 ILE cc_start: 0.8887 (mm) cc_final: 0.8683 (mm) REVERT: E 310 ARG cc_start: 0.6103 (mtt180) cc_final: 0.5886 (mtt90) REVERT: E 443 ILE cc_start: 0.7641 (mm) cc_final: 0.7407 (mm) REVERT: E 448 ASP cc_start: 0.7728 (m-30) cc_final: 0.7288 (m-30) REVERT: E 467 PHE cc_start: 0.7418 (m-10) cc_final: 0.6981 (t80) outliers start: 11 outliers final: 3 residues processed: 368 average time/residue: 0.2478 time to fit residues: 141.6180 Evaluate side-chains 200 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 297 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 305 ASN C 445 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17052 Z= 0.204 Angle : 0.575 8.838 23274 Z= 0.283 Chirality : 0.045 0.279 2806 Planarity : 0.004 0.042 2829 Dihedral : 13.334 90.665 2852 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.56 % Allowed : 10.13 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1970 helix: 2.18 (0.19), residues: 749 sheet: -0.58 (0.25), residues: 407 loop : -0.78 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.006 0.001 HIS A 408 PHE 0.021 0.001 PHE C 478 TYR 0.011 0.001 TYR B 240 ARG 0.006 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8568 (m-40) cc_final: 0.8196 (m110) REVERT: A 179 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7781 (mttm) REVERT: A 238 ASP cc_start: 0.7441 (t0) cc_final: 0.7239 (t0) REVERT: A 252 SER cc_start: 0.9294 (m) cc_final: 0.9040 (p) REVERT: A 324 MET cc_start: 0.7495 (tmm) cc_final: 0.6497 (pmm) REVERT: B 250 SER cc_start: 0.8848 (t) cc_final: 0.8569 (m) REVERT: C 257 MET cc_start: 0.7677 (mmm) cc_final: 0.7315 (tpp) REVERT: C 445 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7158 (t0) REVERT: C 473 PHE cc_start: 0.7737 (m-10) cc_final: 0.6966 (t80) REVERT: D 277 TYR cc_start: 0.7612 (m-10) cc_final: 0.6355 (t80) REVERT: D 410 LEU cc_start: 0.8554 (mm) cc_final: 0.8237 (mm) REVERT: E 239 LEU cc_start: 0.8691 (tp) cc_final: 0.8421 (tp) REVERT: E 257 SER cc_start: 0.8501 (m) cc_final: 0.8292 (m) REVERT: E 310 ARG cc_start: 0.6336 (mtt180) cc_final: 0.6016 (mtt90) outliers start: 47 outliers final: 25 residues processed: 233 average time/residue: 0.2270 time to fit residues: 85.6683 Evaluate side-chains 215 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 176 optimal weight: 0.0030 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 297 ASN B 105 HIS C 231 ASN C 267 GLN C 451 GLN E 250 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17052 Z= 0.261 Angle : 0.569 7.634 23274 Z= 0.281 Chirality : 0.044 0.239 2806 Planarity : 0.004 0.037 2829 Dihedral : 11.901 83.950 2850 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.94 % Allowed : 11.49 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1970 helix: 2.19 (0.19), residues: 756 sheet: -0.59 (0.25), residues: 396 loop : -0.86 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.003 0.001 HIS C 60 PHE 0.019 0.001 PHE C 471 TYR 0.010 0.001 TYR E 117 ARG 0.034 0.001 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7714 (t0) cc_final: 0.7492 (t0) REVERT: A 252 SER cc_start: 0.9304 (m) cc_final: 0.9061 (p) REVERT: A 324 MET cc_start: 0.7459 (tmm) cc_final: 0.6907 (pmm) REVERT: B 94 ASN cc_start: 0.8336 (t0) cc_final: 0.7047 (t0) REVERT: B 250 SER cc_start: 0.8952 (t) cc_final: 0.8700 (m) REVERT: B 285 MET cc_start: 0.7705 (mmm) cc_final: 0.6657 (tmm) REVERT: B 433 MET cc_start: 0.7898 (ttm) cc_final: 0.7686 (ttm) REVERT: B 462 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (m) REVERT: C 11 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 340 MET cc_start: 0.5614 (mmt) cc_final: 0.5220 (mmt) REVERT: C 445 ASN cc_start: 0.7986 (m-40) cc_final: 0.7541 (t0) REVERT: C 473 PHE cc_start: 0.7833 (m-10) cc_final: 0.7017 (t80) REVERT: C 499 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7357 (tpp80) REVERT: D 277 TYR cc_start: 0.7553 (m-10) cc_final: 0.6236 (t80) REVERT: D 410 LEU cc_start: 0.8650 (mm) cc_final: 0.8340 (mm) REVERT: E 239 LEU cc_start: 0.8714 (tp) cc_final: 0.8475 (tp) outliers start: 54 outliers final: 36 residues processed: 237 average time/residue: 0.2270 time to fit residues: 87.1662 Evaluate side-chains 217 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 451 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17052 Z= 0.212 Angle : 0.554 8.294 23274 Z= 0.270 Chirality : 0.044 0.260 2806 Planarity : 0.004 0.034 2829 Dihedral : 10.363 79.912 2850 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 12.96 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1970 helix: 2.27 (0.19), residues: 749 sheet: -0.64 (0.24), residues: 407 loop : -0.84 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.005 0.001 HIS A 186 PHE 0.025 0.001 PHE C 478 TYR 0.010 0.001 TYR E 117 ARG 0.004 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 191 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6253 (mt-10) REVERT: A 252 SER cc_start: 0.9283 (m) cc_final: 0.9050 (p) REVERT: A 280 PHE cc_start: 0.7576 (t80) cc_final: 0.6581 (m-10) REVERT: A 400 LYS cc_start: 0.8547 (mttt) cc_final: 0.8135 (mtmm) REVERT: B 94 ASN cc_start: 0.8228 (t0) cc_final: 0.6915 (t0) REVERT: B 285 MET cc_start: 0.7635 (mmm) cc_final: 0.6745 (tmm) REVERT: C 255 GLU cc_start: 0.7945 (tp30) cc_final: 0.7254 (tp30) REVERT: C 445 ASN cc_start: 0.7677 (m-40) cc_final: 0.7191 (t0) REVERT: C 465 MET cc_start: 0.8379 (ptp) cc_final: 0.8151 (ptp) REVERT: C 473 PHE cc_start: 0.7902 (m-10) cc_final: 0.7014 (t80) REVERT: C 499 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7303 (mtm180) REVERT: D 277 TYR cc_start: 0.7372 (m-10) cc_final: 0.6093 (t80) REVERT: D 308 MET cc_start: 0.6589 (tpt) cc_final: 0.6375 (tpt) REVERT: D 410 LEU cc_start: 0.8656 (mm) cc_final: 0.8366 (mm) REVERT: E 239 LEU cc_start: 0.8754 (tp) cc_final: 0.8493 (tp) REVERT: E 310 ARG cc_start: 0.6223 (mtt90) cc_final: 0.5869 (mtt90) outliers start: 52 outliers final: 33 residues processed: 228 average time/residue: 0.2301 time to fit residues: 85.1352 Evaluate side-chains 215 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 451 GLN E 250 GLN E 262 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17052 Z= 0.163 Angle : 0.528 8.199 23274 Z= 0.257 Chirality : 0.043 0.212 2806 Planarity : 0.003 0.035 2829 Dihedral : 9.478 71.049 2850 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.56 % Allowed : 13.50 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1970 helix: 2.36 (0.19), residues: 749 sheet: -0.58 (0.25), residues: 398 loop : -0.85 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 PHE 0.019 0.001 PHE C 471 TYR 0.011 0.001 TYR E 117 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7684 (mm-40) REVERT: A 280 PHE cc_start: 0.7529 (t80) cc_final: 0.6628 (m-10) REVERT: A 324 MET cc_start: 0.7464 (tmm) cc_final: 0.6502 (pmm) REVERT: A 400 LYS cc_start: 0.8530 (mttt) cc_final: 0.8063 (mtmm) REVERT: B 94 ASN cc_start: 0.8017 (t0) cc_final: 0.6467 (t0) REVERT: B 285 MET cc_start: 0.7592 (mmm) cc_final: 0.6700 (tmm) REVERT: C 249 LEU cc_start: 0.7614 (mp) cc_final: 0.7329 (mp) REVERT: C 293 MET cc_start: 0.7822 (mmm) cc_final: 0.7590 (mmm) REVERT: C 445 ASN cc_start: 0.7624 (m-40) cc_final: 0.7043 (t0) REVERT: C 465 MET cc_start: 0.8266 (ptp) cc_final: 0.8024 (ptp) REVERT: C 473 PHE cc_start: 0.7805 (m-10) cc_final: 0.6953 (t80) REVERT: C 499 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7265 (mtm180) REVERT: D 277 TYR cc_start: 0.7437 (m-10) cc_final: 0.6124 (t80) REVERT: D 410 LEU cc_start: 0.8641 (mm) cc_final: 0.8389 (mm) REVERT: E 239 LEU cc_start: 0.8688 (tp) cc_final: 0.8457 (tp) REVERT: E 310 ARG cc_start: 0.6244 (mtt90) cc_final: 0.5884 (mtt90) outliers start: 47 outliers final: 27 residues processed: 225 average time/residue: 0.2274 time to fit residues: 83.2526 Evaluate side-chains 209 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17052 Z= 0.405 Angle : 0.648 7.416 23274 Z= 0.321 Chirality : 0.047 0.246 2806 Planarity : 0.004 0.036 2829 Dihedral : 9.119 62.592 2850 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.21 % Allowed : 13.66 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1970 helix: 2.06 (0.19), residues: 757 sheet: -0.73 (0.24), residues: 398 loop : -0.93 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 120 HIS 0.005 0.001 HIS E 27 PHE 0.026 0.002 PHE C 478 TYR 0.011 0.002 TYR C 102 ARG 0.008 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.7599 (t80) cc_final: 0.6689 (m-10) REVERT: A 324 MET cc_start: 0.7570 (tmm) cc_final: 0.6676 (pmm) REVERT: A 400 LYS cc_start: 0.8661 (mttt) cc_final: 0.8193 (mtmm) REVERT: B 94 ASN cc_start: 0.8514 (t0) cc_final: 0.8125 (t0) REVERT: B 285 MET cc_start: 0.7605 (mmm) cc_final: 0.6754 (tmm) REVERT: C 445 ASN cc_start: 0.7674 (m-40) cc_final: 0.6990 (t0) REVERT: C 499 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7337 (mtm180) REVERT: D 410 LEU cc_start: 0.8836 (mm) cc_final: 0.8532 (mm) REVERT: E 239 LEU cc_start: 0.8782 (tp) cc_final: 0.8541 (tp) outliers start: 59 outliers final: 40 residues processed: 219 average time/residue: 0.2382 time to fit residues: 84.3289 Evaluate side-chains 212 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 451 GLN E 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17052 Z= 0.188 Angle : 0.536 8.556 23274 Z= 0.265 Chirality : 0.043 0.210 2806 Planarity : 0.004 0.037 2829 Dihedral : 8.238 59.974 2850 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.34 % Allowed : 15.08 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1970 helix: 2.21 (0.19), residues: 758 sheet: -0.72 (0.25), residues: 397 loop : -0.87 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 PHE 0.018 0.001 PHE C 471 TYR 0.010 0.001 TYR E 117 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.7590 (t80) cc_final: 0.6684 (m-10) REVERT: A 324 MET cc_start: 0.7472 (tmm) cc_final: 0.6637 (pmm) REVERT: A 400 LYS cc_start: 0.8649 (mttt) cc_final: 0.8167 (mtmm) REVERT: B 285 MET cc_start: 0.7599 (mmm) cc_final: 0.6749 (tmm) REVERT: C 445 ASN cc_start: 0.7604 (m-40) cc_final: 0.6858 (t0) REVERT: C 465 MET cc_start: 0.8356 (ptp) cc_final: 0.8120 (ptp) REVERT: C 499 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7276 (mtm180) REVERT: D 228 LEU cc_start: 0.9049 (mt) cc_final: 0.8837 (mt) REVERT: D 410 LEU cc_start: 0.8812 (mm) cc_final: 0.8520 (mm) REVERT: E 239 LEU cc_start: 0.8776 (tp) cc_final: 0.8545 (tp) REVERT: E 310 ARG cc_start: 0.6665 (mtt90) cc_final: 0.6124 (mtt180) outliers start: 43 outliers final: 36 residues processed: 213 average time/residue: 0.2272 time to fit residues: 78.6783 Evaluate side-chains 211 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 421 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN B 87 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17052 Z= 0.177 Angle : 0.523 6.742 23274 Z= 0.259 Chirality : 0.043 0.229 2806 Planarity : 0.004 0.036 2829 Dihedral : 7.537 56.755 2850 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 15.41 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1970 helix: 2.21 (0.19), residues: 763 sheet: -0.68 (0.25), residues: 399 loop : -0.86 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.004 0.001 HIS C 60 PHE 0.030 0.001 PHE C 478 TYR 0.009 0.001 TYR E 117 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7621 (mm-40) REVERT: A 280 PHE cc_start: 0.7426 (t80) cc_final: 0.6564 (m-10) REVERT: A 400 LYS cc_start: 0.8631 (mttt) cc_final: 0.8129 (mtmm) REVERT: B 285 MET cc_start: 0.7669 (mmm) cc_final: 0.6788 (tmm) REVERT: C 249 LEU cc_start: 0.7707 (mp) cc_final: 0.7297 (mp) REVERT: C 445 ASN cc_start: 0.7616 (m-40) cc_final: 0.6889 (t0) REVERT: C 499 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7234 (mtm180) REVERT: D 410 LEU cc_start: 0.8822 (mm) cc_final: 0.8531 (mm) REVERT: E 239 LEU cc_start: 0.8759 (tp) cc_final: 0.8535 (tp) REVERT: E 310 ARG cc_start: 0.6623 (mtt90) cc_final: 0.6128 (mtt90) REVERT: E 451 CYS cc_start: 0.8401 (m) cc_final: 0.7521 (p) outliers start: 44 outliers final: 35 residues processed: 220 average time/residue: 0.2288 time to fit residues: 81.4667 Evaluate side-chains 218 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 421 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 0.0970 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 54 optimal weight: 0.0270 chunk 159 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 451 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17052 Z= 0.148 Angle : 0.517 9.030 23274 Z= 0.256 Chirality : 0.042 0.223 2806 Planarity : 0.003 0.036 2829 Dihedral : 7.110 58.112 2850 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.85 % Allowed : 15.84 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1970 helix: 2.34 (0.19), residues: 757 sheet: -0.58 (0.25), residues: 390 loop : -0.82 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.005 0.000 HIS C 60 PHE 0.024 0.001 PHE A 284 TYR 0.010 0.001 TYR E 117 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8350 (tmm) cc_final: 0.8009 (tmm) REVERT: A 280 PHE cc_start: 0.7341 (t80) cc_final: 0.6608 (m-10) REVERT: A 324 MET cc_start: 0.7426 (tmm) cc_final: 0.6357 (pmm) REVERT: A 400 LYS cc_start: 0.8611 (mttt) cc_final: 0.8112 (mtmm) REVERT: B 285 MET cc_start: 0.7718 (mmm) cc_final: 0.6831 (tmm) REVERT: C 249 LEU cc_start: 0.7719 (mp) cc_final: 0.7293 (mp) REVERT: C 261 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7764 (mp) REVERT: C 445 ASN cc_start: 0.7594 (m-40) cc_final: 0.6961 (t0) REVERT: C 465 MET cc_start: 0.8439 (ptp) cc_final: 0.8206 (ptp) REVERT: C 499 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7202 (mtm180) REVERT: D 410 LEU cc_start: 0.8806 (mm) cc_final: 0.8534 (mm) REVERT: E 239 LEU cc_start: 0.8720 (tp) cc_final: 0.8515 (tp) REVERT: E 310 ARG cc_start: 0.6528 (mtt90) cc_final: 0.5909 (mtt90) REVERT: E 451 CYS cc_start: 0.8380 (m) cc_final: 0.7525 (p) outliers start: 34 outliers final: 28 residues processed: 220 average time/residue: 0.2371 time to fit residues: 84.5973 Evaluate side-chains 217 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 421 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 0.0070 chunk 179 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17052 Z= 0.194 Angle : 0.535 8.945 23274 Z= 0.266 Chirality : 0.043 0.238 2806 Planarity : 0.004 0.035 2829 Dihedral : 7.061 59.586 2850 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 16.22 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1970 helix: 2.25 (0.19), residues: 763 sheet: -0.57 (0.25), residues: 395 loop : -0.79 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 187 HIS 0.005 0.001 HIS C 60 PHE 0.031 0.001 PHE C 478 TYR 0.012 0.001 TYR C 439 ARG 0.003 0.000 ARG A 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.7374 (t80) cc_final: 0.6508 (m-10) REVERT: A 324 MET cc_start: 0.7306 (tmm) cc_final: 0.6179 (pmm) REVERT: A 400 LYS cc_start: 0.8629 (mttt) cc_final: 0.8124 (mtmm) REVERT: B 285 MET cc_start: 0.7688 (mmm) cc_final: 0.6811 (tmm) REVERT: C 249 LEU cc_start: 0.7687 (mp) cc_final: 0.7290 (mp) REVERT: C 261 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7735 (mp) REVERT: C 445 ASN cc_start: 0.7626 (m-40) cc_final: 0.6995 (t0) REVERT: C 499 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7260 (mtm180) REVERT: D 178 MET cc_start: 0.9010 (mmp) cc_final: 0.8220 (mmt) REVERT: D 308 MET cc_start: 0.6569 (tpt) cc_final: 0.6313 (tpt) REVERT: D 410 LEU cc_start: 0.8844 (mm) cc_final: 0.8568 (mm) REVERT: E 239 LEU cc_start: 0.8744 (tp) cc_final: 0.8540 (tp) REVERT: E 310 ARG cc_start: 0.6506 (mtt90) cc_final: 0.5794 (mtt90) REVERT: E 451 CYS cc_start: 0.8402 (m) cc_final: 0.7566 (p) outliers start: 36 outliers final: 29 residues processed: 209 average time/residue: 0.2279 time to fit residues: 77.9619 Evaluate side-chains 214 residues out of total 1837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 421 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085889 restraints weight = 32988.312| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.85 r_work: 0.3036 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17052 Z= 0.209 Angle : 0.541 8.231 23274 Z= 0.271 Chirality : 0.043 0.229 2806 Planarity : 0.004 0.036 2829 Dihedral : 6.991 58.938 2850 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 16.39 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1970 helix: 2.23 (0.19), residues: 762 sheet: -0.50 (0.25), residues: 388 loop : -0.77 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 PHE 0.023 0.001 PHE C 471 TYR 0.013 0.001 TYR C 439 ARG 0.003 0.000 ARG A 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.06 seconds wall clock time: 61 minutes 1.65 seconds (3661.65 seconds total)