Starting phenix.real_space_refine on Tue Apr 9 03:43:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/04_2024/8dn3_27553_trim_updated.pdb" } resolution = 3.55 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= 0.008 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 9467 2.51 5 N 2270 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14315 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2762 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2796 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2768 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2785 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2707 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Unusual residues: {'DD9': 1, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 4} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Unusual residues: {'DD9': 2, 'HEX': 4, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Unusual residues: {'DD9': 5, 'HEX': 3, 'NAG': 1, 'NBU': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 116 Unusual residues: {'D10': 1, 'DD9': 3, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 90 Unusual residues: {' CL': 2, 'DD9': 2, 'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.89, per 1000 atoms: 0.55 Number of scatterers: 14315 At special positions: 0 Unit cell: (103.75, 127.82, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2474 8.00 N 2270 7.00 C 9467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " 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=5, symmetry=0 Links applied NAG-ASN " NAG C 503 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 504 " - " ASN E 220 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.88 Conformation dependent library (CDL) restraints added in 2.6 seconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 20 sheets defined 35.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'D' and resid 10 through 17 removed outlier: 3.536A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 4.704A pdb=" N SER D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 242 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 249 through 273 removed outlier: 4.049A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 308 removed outlier: 3.962A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 418 removed outlier: 4.280A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.617A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.620A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'A' and resid 386 through 418 removed outlier: 3.961A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 87 through 92 removed outlier: 4.558A pdb=" N SER B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.602A pdb=" N ARG B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 Processing helix chain 'B' and resid 386 through 418 removed outlier: 3.789A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Proline residue: B 403 - end of helix removed outlier: 3.625A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.583A pdb=" N SER C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 242 Proline residue: C 230 - end of helix removed outlier: 4.165A pdb=" N PHE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 273 Processing helix chain 'C' and resid 284 through 312 removed outlier: 3.919A pdb=" N HIS C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 416 removed outlier: 3.748A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.614A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 252 through 267 removed outlier: 3.820A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 294 Proline residue: E 278 - end of helix Processing helix chain 'E' and resid 306 through 332 Processing helix chain 'E' and resid 449 through 474 removed outlier: 3.805A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id= A, first strand: chain 'D' and resid 166 through 169 removed outlier: 5.929A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 107 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.904A pdb=" N ILE D 43 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= E, first strand: chain 'D' and resid 199 through 202 removed outlier: 3.507A pdb=" N LYS D 200 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.336A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.589A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= J, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.428A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 65 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 149 through 157 removed outlier: 3.576A pdb=" N LYS B 200 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS B 209 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS B 198 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.320A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 166 through 169 removed outlier: 6.383A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.093A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.875A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS C 209 " --> pdb=" O CYS C 198 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 45 through 49 removed outlier: 6.331A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 189 through 193 removed outlier: 6.474A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 121 through 123 Processing sheet with id= S, first strand: chain 'E' and resid 172 through 176 Processing sheet with id= T, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.540A pdb=" N LYS E 223 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1680 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: 3.96 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4181 1.34 - 1.46: 2289 1.46 - 1.57: 7965 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 14607 Sorted by residual: bond pdb=" N GLN D 310 " pdb=" CA GLN D 310 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.41e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.35e+00 bond pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 14602 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 436 106.62 - 113.46: 7631 113.46 - 120.31: 5441 120.31 - 127.15: 5935 127.15 - 134.00: 169 Bond angle restraints: 19612 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 112.89 107.11 5.78 1.24e+00 6.50e-01 2.17e+01 angle pdb=" CA HIS A 311 " pdb=" C HIS A 311 " pdb=" O HIS A 311 " ideal model delta sigma weight residual 121.19 117.38 3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" CA THR A 258 " pdb=" C THR A 258 " pdb=" O THR A 258 " ideal model delta sigma weight residual 120.82 117.49 3.33 1.05e+00 9.07e-01 1.01e+01 angle pdb=" N GLN A 310 " pdb=" CA GLN A 310 " pdb=" C GLN A 310 " ideal model delta sigma weight residual 111.71 108.07 3.64 1.15e+00 7.56e-01 1.00e+01 angle pdb=" N PHE D 412 " pdb=" CA PHE D 412 " pdb=" C PHE D 412 " ideal model delta sigma weight residual 112.89 109.00 3.89 1.24e+00 6.50e-01 9.85e+00 ... (remaining 19607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 8530 24.23 - 48.47: 273 48.47 - 72.70: 18 72.70 - 96.93: 11 96.93 - 121.16: 6 Dihedral angle restraints: 8838 sinusoidal: 3821 harmonic: 5017 Sorted by residual: dihedral pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " pdb=" C5 DD9 A 508 " pdb=" C6 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.92 58.76 121.16 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C1 DD9 A 508 " pdb=" C2 DD9 A 508 " pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.94 -67.82 -112.24 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C2 NAG E 504 " pdb=" C3 NAG E 504 " pdb=" C4 NAG E 504 " pdb=" C5 NAG E 504 " ideal model delta sinusoidal sigma weight residual 53.78 -48.09 101.87 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2154 0.173 - 0.346: 1 0.346 - 0.519: 0 0.519 - 0.692: 0 0.692 - 0.865: 1 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 38 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 2153 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.321 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C7 NAG A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.003 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.292 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG D 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" C7 NAG C 503 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " 0.396 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " -0.008 2.00e-02 2.50e+03 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 663 2.73 - 3.27: 14126 3.27 - 3.81: 22531 3.81 - 4.36: 26937 4.36 - 4.90: 46932 Nonbonded interactions: 111189 Sorted by model distance: nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR B 112 " model vdw 2.181 2.440 nonbonded pdb=" O ALA D 282 " pdb=" OH TYR D 413 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 112 " pdb=" O LEU E 121 " model vdw 2.234 2.440 nonbonded pdb=" O LEU B 98 " pdb=" OG1 THR C 112 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.238 2.440 ... (remaining 111184 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 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 310 or resid 384 through 419)) selection = (chain 'D' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.630 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.400 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.003 0.038 14607 Z= 0.220 Angle : 0.565 8.288 19612 Z= 0.287 Chirality : 0.046 0.865 2156 Planarity : 0.009 0.274 2412 Dihedral : 11.886 121.162 5559 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 5.51 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1679 helix: 2.25 (0.22), residues: 583 sheet: -0.40 (0.30), residues: 359 loop : -0.75 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 243 HIS 0.002 0.000 HIS A 311 PHE 0.010 0.001 PHE D 242 TYR 0.017 0.001 TYR E 325 ARG 0.002 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8081 (t70) cc_final: 0.7671 (p0) REVERT: D 246 MET cc_start: 0.7313 (mtm) cc_final: 0.7076 (mtt) REVERT: A 91 ASP cc_start: 0.8812 (t0) cc_final: 0.8612 (t0) REVERT: A 169 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 173 GLN cc_start: 0.8343 (pp30) cc_final: 0.8086 (pp30) REVERT: A 203 ASN cc_start: 0.8690 (m-40) cc_final: 0.8006 (p0) REVERT: A 396 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7571 (mtmm) REVERT: A 400 ILE cc_start: 0.8271 (tp) cc_final: 0.7582 (pt) REVERT: B 18 MET cc_start: 0.8467 (ppp) cc_final: 0.8112 (ptt) REVERT: B 83 LEU cc_start: 0.7978 (tt) cc_final: 0.7710 (tt) REVERT: B 397 ILE cc_start: 0.8516 (mm) cc_final: 0.8249 (mt) REVERT: B 411 MET cc_start: 0.7501 (mmp) cc_final: 0.6547 (ttp) REVERT: C 191 GLU cc_start: 0.8209 (tp30) cc_final: 0.7933 (tp30) REVERT: E 176 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8196 (mmtt) REVERT: E 187 ASP cc_start: 0.8308 (t0) cc_final: 0.7799 (t0) REVERT: E 329 GLN cc_start: 0.8469 (tp40) cc_final: 0.8204 (tp40) outliers start: 30 outliers final: 12 residues processed: 357 average time/residue: 0.2611 time to fit residues: 137.1198 Evaluate side-chains 261 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 0.0770 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN D 201 HIS B 226 GLN C 155 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14607 Z= 0.221 Angle : 0.585 9.425 19612 Z= 0.288 Chirality : 0.044 0.320 2156 Planarity : 0.004 0.037 2412 Dihedral : 7.092 66.179 2242 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 2.69 % Allowed : 11.08 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1679 helix: 2.19 (0.21), residues: 589 sheet: -0.15 (0.31), residues: 339 loop : -0.92 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 243 HIS 0.003 0.001 HIS A 311 PHE 0.012 0.001 PHE E 84 TYR 0.020 0.001 TYR E 325 ARG 0.014 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 251 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8130 (t70) cc_final: 0.7730 (p0) REVERT: D 246 MET cc_start: 0.7430 (mtm) cc_final: 0.7152 (mtt) REVERT: D 263 MET cc_start: 0.8563 (mmm) cc_final: 0.8142 (tmm) REVERT: D 298 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 169 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 173 GLN cc_start: 0.8443 (pp30) cc_final: 0.8131 (pp30) REVERT: A 271 ARG cc_start: 0.8116 (tpt90) cc_final: 0.7865 (tpp80) REVERT: A 396 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7489 (mtmm) REVERT: A 400 ILE cc_start: 0.8262 (tp) cc_final: 0.7634 (pt) REVERT: A 411 MET cc_start: 0.6757 (mmp) cc_final: 0.6356 (mmp) REVERT: B 18 MET cc_start: 0.8472 (ppp) cc_final: 0.8219 (ptt) REVERT: B 397 ILE cc_start: 0.8487 (mm) cc_final: 0.8227 (mt) REVERT: B 411 MET cc_start: 0.7550 (mmp) cc_final: 0.6518 (ttp) REVERT: C 191 GLU cc_start: 0.8255 (tp30) cc_final: 0.8011 (tp30) REVERT: C 206 LYS cc_start: 0.7393 (mptt) cc_final: 0.6744 (mtmt) REVERT: E 88 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7655 (tttp) REVERT: E 176 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8114 (mmtt) REVERT: E 187 ASP cc_start: 0.8330 (t0) cc_final: 0.7790 (t0) REVERT: E 248 MET cc_start: 0.8692 (tpp) cc_final: 0.8232 (tpp) outliers start: 41 outliers final: 29 residues processed: 276 average time/residue: 0.2493 time to fit residues: 103.5050 Evaluate side-chains 260 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 0.0020 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.0470 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 151 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14607 Z= 0.123 Angle : 0.532 9.318 19612 Z= 0.260 Chirality : 0.042 0.274 2156 Planarity : 0.003 0.036 2412 Dihedral : 5.545 58.917 2231 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.49 % Allowed : 13.05 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1679 helix: 2.39 (0.21), residues: 584 sheet: 0.01 (0.31), residues: 348 loop : -0.84 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 243 HIS 0.002 0.000 HIS D 109 PHE 0.011 0.001 PHE C 13 TYR 0.023 0.001 TYR E 224 ARG 0.005 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8098 (t70) cc_final: 0.7600 (p0) REVERT: D 246 MET cc_start: 0.7376 (mtm) cc_final: 0.7123 (mtt) REVERT: A 173 GLN cc_start: 0.8430 (pp30) cc_final: 0.8110 (pp30) REVERT: A 220 MET cc_start: 0.7915 (mmm) cc_final: 0.7479 (mmm) REVERT: A 396 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7738 (mtmm) REVERT: A 400 ILE cc_start: 0.8131 (tp) cc_final: 0.7441 (pt) REVERT: A 411 MET cc_start: 0.6681 (mmp) cc_final: 0.6319 (mmp) REVERT: B 18 MET cc_start: 0.8446 (ppp) cc_final: 0.8172 (ptt) REVERT: B 227 MET cc_start: 0.7980 (mmm) cc_final: 0.7692 (mmt) REVERT: B 266 GLN cc_start: 0.8129 (tp40) cc_final: 0.7878 (tt0) REVERT: B 397 ILE cc_start: 0.8427 (mm) cc_final: 0.8123 (mt) REVERT: B 411 MET cc_start: 0.7421 (mmp) cc_final: 0.6418 (ttp) REVERT: C 206 LYS cc_start: 0.7482 (mptt) cc_final: 0.6829 (mtmt) REVERT: E 176 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7966 (mmtt) REVERT: E 187 ASP cc_start: 0.8336 (t0) cc_final: 0.7831 (t0) REVERT: E 237 ILE cc_start: 0.8792 (mt) cc_final: 0.8553 (mt) REVERT: E 248 MET cc_start: 0.8611 (tpp) cc_final: 0.8114 (tpp) outliers start: 38 outliers final: 25 residues processed: 291 average time/residue: 0.2534 time to fit residues: 109.9967 Evaluate side-chains 261 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.0770 chunk 114 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 0.0470 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14607 Z= 0.117 Angle : 0.515 8.494 19612 Z= 0.252 Chirality : 0.041 0.251 2156 Planarity : 0.003 0.045 2412 Dihedral : 5.173 58.152 2228 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 3.02 % Allowed : 13.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1679 helix: 2.35 (0.21), residues: 590 sheet: -0.05 (0.30), residues: 354 loop : -0.84 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 243 HIS 0.002 0.000 HIS A 311 PHE 0.010 0.001 PHE C 13 TYR 0.015 0.001 TYR E 224 ARG 0.004 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8092 (t70) cc_final: 0.7521 (p0) REVERT: D 246 MET cc_start: 0.7371 (mtm) cc_final: 0.7133 (mtt) REVERT: A 173 GLN cc_start: 0.8440 (pp30) cc_final: 0.8105 (pp30) REVERT: A 400 ILE cc_start: 0.8217 (tp) cc_final: 0.7602 (pt) REVERT: A 411 MET cc_start: 0.6658 (mmp) cc_final: 0.6355 (mmp) REVERT: B 18 MET cc_start: 0.8414 (ppp) cc_final: 0.8153 (ptt) REVERT: B 227 MET cc_start: 0.8119 (mmm) cc_final: 0.7889 (mmt) REVERT: B 266 GLN cc_start: 0.8044 (tp40) cc_final: 0.7810 (tt0) REVERT: B 411 MET cc_start: 0.7385 (mmp) cc_final: 0.6405 (ttp) REVERT: C 147 MET cc_start: 0.8918 (mtm) cc_final: 0.8447 (mpp) REVERT: C 206 LYS cc_start: 0.7481 (mptt) cc_final: 0.6844 (mtmt) REVERT: E 116 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8283 (pp) REVERT: E 176 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7966 (mmtt) REVERT: E 187 ASP cc_start: 0.8326 (t0) cc_final: 0.7831 (t0) REVERT: E 450 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7409 (mtm-85) outliers start: 46 outliers final: 30 residues processed: 279 average time/residue: 0.2454 time to fit residues: 102.4604 Evaluate side-chains 273 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 0.0050 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 186 GLN D 201 HIS B 155 GLN C 42 ASN C 46 ASN C 150 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14607 Z= 0.414 Angle : 0.658 9.287 19612 Z= 0.334 Chirality : 0.046 0.230 2156 Planarity : 0.004 0.036 2412 Dihedral : 6.516 55.204 2228 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 4.20 % Allowed : 14.16 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1679 helix: 1.96 (0.21), residues: 590 sheet: -0.42 (0.29), residues: 375 loop : -0.93 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 243 HIS 0.004 0.001 HIS A 311 PHE 0.021 0.002 PHE B 48 TYR 0.030 0.002 TYR A 301 ARG 0.004 0.001 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8153 (t70) cc_final: 0.7709 (p0) REVERT: A 169 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 173 GLN cc_start: 0.8516 (pp30) cc_final: 0.8135 (pp30) REVERT: A 396 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8125 (mmtt) REVERT: A 411 MET cc_start: 0.6719 (mmt) cc_final: 0.6264 (mmp) REVERT: C 42 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8281 (p0) REVERT: C 206 LYS cc_start: 0.7471 (mptt) cc_final: 0.6794 (mtmt) REVERT: E 88 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7631 (tttt) REVERT: E 141 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8277 (tt) REVERT: E 176 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 187 ASP cc_start: 0.8438 (t0) cc_final: 0.7927 (t0) outliers start: 64 outliers final: 42 residues processed: 273 average time/residue: 0.2539 time to fit residues: 103.6331 Evaluate side-chains 260 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN C 150 GLN C 305 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14607 Z= 0.174 Angle : 0.564 8.924 19612 Z= 0.280 Chirality : 0.042 0.194 2156 Planarity : 0.003 0.036 2412 Dihedral : 6.113 59.312 2228 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 3.41 % Allowed : 16.46 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1679 helix: 2.22 (0.22), residues: 590 sheet: -0.30 (0.30), residues: 363 loop : -0.90 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 243 HIS 0.002 0.001 HIS A 311 PHE 0.014 0.001 PHE C 306 TYR 0.028 0.001 TYR E 224 ARG 0.005 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8131 (t70) cc_final: 0.7629 (p0) REVERT: A 169 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 173 GLN cc_start: 0.8520 (pp30) cc_final: 0.8137 (pp30) REVERT: A 411 MET cc_start: 0.6720 (mmt) cc_final: 0.6373 (mmp) REVERT: B 227 MET cc_start: 0.8004 (mmm) cc_final: 0.7695 (mmt) REVERT: B 266 GLN cc_start: 0.8112 (tp40) cc_final: 0.7750 (tt0) REVERT: B 411 MET cc_start: 0.7535 (mmp) cc_final: 0.6421 (ttp) REVERT: C 206 LYS cc_start: 0.7485 (mptt) cc_final: 0.6822 (mtmt) REVERT: E 141 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8238 (tt) REVERT: E 176 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8015 (mmtt) REVERT: E 187 ASP cc_start: 0.8400 (t0) cc_final: 0.7884 (t0) outliers start: 52 outliers final: 36 residues processed: 272 average time/residue: 0.2463 time to fit residues: 101.3727 Evaluate side-chains 270 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 0.0030 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14607 Z= 0.283 Angle : 0.587 8.712 19612 Z= 0.294 Chirality : 0.043 0.180 2156 Planarity : 0.004 0.054 2412 Dihedral : 6.254 58.706 2228 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 3.15 % Allowed : 17.31 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1679 helix: 2.16 (0.22), residues: 591 sheet: -0.35 (0.29), residues: 372 loop : -0.90 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D 243 HIS 0.003 0.001 HIS A 311 PHE 0.021 0.001 PHE C 13 TYR 0.031 0.002 TYR E 224 ARG 0.006 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 225 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8182 (t70) cc_final: 0.7709 (p0) REVERT: A 169 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 173 GLN cc_start: 0.8534 (pp30) cc_final: 0.8132 (pp30) REVERT: A 411 MET cc_start: 0.6715 (mmt) cc_final: 0.6318 (mmp) REVERT: B 227 MET cc_start: 0.8006 (mmm) cc_final: 0.7734 (mmt) REVERT: C 57 ASP cc_start: 0.8518 (p0) cc_final: 0.8132 (p0) REVERT: C 206 LYS cc_start: 0.7461 (mptt) cc_final: 0.6804 (mtmt) REVERT: E 141 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8294 (tt) REVERT: E 176 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8092 (mmtt) REVERT: E 187 ASP cc_start: 0.8439 (t0) cc_final: 0.7917 (t0) outliers start: 48 outliers final: 42 residues processed: 255 average time/residue: 0.2487 time to fit residues: 94.7092 Evaluate side-chains 261 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14607 Z= 0.160 Angle : 0.551 8.477 19612 Z= 0.271 Chirality : 0.042 0.178 2156 Planarity : 0.004 0.052 2412 Dihedral : 5.849 59.336 2228 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.02 % Allowed : 17.44 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1679 helix: 2.26 (0.22), residues: 591 sheet: -0.26 (0.29), residues: 369 loop : -0.84 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 243 HIS 0.006 0.001 HIS D 311 PHE 0.010 0.001 PHE E 84 TYR 0.032 0.001 TYR E 224 ARG 0.006 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8153 (t70) cc_final: 0.7611 (p0) REVERT: D 386 LEU cc_start: 0.8158 (pt) cc_final: 0.7544 (tt) REVERT: A 169 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 173 GLN cc_start: 0.8537 (pp30) cc_final: 0.8136 (pp30) REVERT: A 247 ASP cc_start: 0.7959 (t70) cc_final: 0.7711 (t0) REVERT: A 396 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7760 (mmtt) REVERT: A 400 ILE cc_start: 0.8506 (tp) cc_final: 0.8044 (tp) REVERT: A 411 MET cc_start: 0.6657 (mmt) cc_final: 0.6297 (mmp) REVERT: B 227 MET cc_start: 0.8144 (mmm) cc_final: 0.7645 (mmt) REVERT: C 206 LYS cc_start: 0.7471 (mptt) cc_final: 0.6830 (mtmt) REVERT: C 287 MET cc_start: 0.8388 (mmt) cc_final: 0.8120 (mmt) REVERT: E 141 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 176 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8029 (mmtt) REVERT: E 187 ASP cc_start: 0.8407 (t0) cc_final: 0.7894 (t0) REVERT: E 316 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8221 (mp) outliers start: 46 outliers final: 38 residues processed: 275 average time/residue: 0.2483 time to fit residues: 102.1577 Evaluate side-chains 272 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14607 Z= 0.167 Angle : 0.547 8.527 19612 Z= 0.269 Chirality : 0.041 0.163 2156 Planarity : 0.003 0.035 2412 Dihedral : 5.628 59.981 2228 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.89 % Allowed : 18.16 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1679 helix: 2.27 (0.22), residues: 591 sheet: -0.24 (0.29), residues: 373 loop : -0.82 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 243 HIS 0.004 0.001 HIS D 311 PHE 0.012 0.001 PHE C 13 TYR 0.032 0.001 TYR E 224 ARG 0.006 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8163 (t70) cc_final: 0.7609 (p0) REVERT: D 386 LEU cc_start: 0.8134 (pt) cc_final: 0.7542 (tt) REVERT: D 400 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 173 GLN cc_start: 0.8562 (pp30) cc_final: 0.8153 (pp30) REVERT: A 400 ILE cc_start: 0.8530 (tp) cc_final: 0.8069 (tp) REVERT: A 411 MET cc_start: 0.6659 (mmt) cc_final: 0.6293 (mmp) REVERT: C 206 LYS cc_start: 0.7471 (mptt) cc_final: 0.6832 (mtmt) REVERT: E 141 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 176 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8054 (mmtt) REVERT: E 187 ASP cc_start: 0.8396 (t0) cc_final: 0.7896 (t0) outliers start: 44 outliers final: 40 residues processed: 265 average time/residue: 0.2381 time to fit residues: 96.1356 Evaluate side-chains 268 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 0.0470 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14607 Z= 0.144 Angle : 0.545 8.376 19612 Z= 0.267 Chirality : 0.041 0.162 2156 Planarity : 0.003 0.036 2412 Dihedral : 5.408 58.806 2228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.08 % Allowed : 18.16 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1679 helix: 2.28 (0.22), residues: 591 sheet: -0.17 (0.29), residues: 373 loop : -0.86 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 243 HIS 0.003 0.000 HIS D 311 PHE 0.012 0.001 PHE C 13 TYR 0.032 0.001 TYR E 224 ARG 0.006 0.000 ARG D 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8185 (t70) cc_final: 0.7605 (p0) REVERT: D 386 LEU cc_start: 0.8069 (pt) cc_final: 0.7490 (tt) REVERT: A 173 GLN cc_start: 0.8567 (pp30) cc_final: 0.8155 (pp30) REVERT: A 396 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7748 (mmtt) REVERT: A 400 ILE cc_start: 0.8508 (tp) cc_final: 0.8081 (tp) REVERT: A 411 MET cc_start: 0.6592 (mmt) cc_final: 0.6233 (mmp) REVERT: C 206 LYS cc_start: 0.7462 (mptt) cc_final: 0.6825 (mtmt) REVERT: E 141 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8143 (tt) REVERT: E 176 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8077 (mmtt) REVERT: E 187 ASP cc_start: 0.8384 (t0) cc_final: 0.7893 (t0) REVERT: E 282 PHE cc_start: 0.8682 (m-80) cc_final: 0.8461 (m-80) REVERT: E 316 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 47 outliers final: 41 residues processed: 269 average time/residue: 0.2460 time to fit residues: 100.6146 Evaluate side-chains 276 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110463 restraints weight = 20998.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114561 restraints weight = 10263.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117348 restraints weight = 6494.897| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14607 Z= 0.134 Angle : 0.542 9.293 19612 Z= 0.263 Chirality : 0.041 0.157 2156 Planarity : 0.003 0.036 2412 Dihedral : 5.130 57.726 2228 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.62 % Allowed : 18.75 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1679 helix: 2.28 (0.22), residues: 590 sheet: -0.16 (0.28), residues: 379 loop : -0.82 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 243 HIS 0.002 0.000 HIS A 311 PHE 0.014 0.001 PHE A 295 TYR 0.032 0.001 TYR E 224 ARG 0.006 0.000 ARG D 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.20 seconds wall clock time: 56 minutes 0.24 seconds (3360.24 seconds total)