Starting phenix.real_space_refine on Tue Dec 31 07:24:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn5_27555/12_2024/8dn5_27555_trim.cif" } resolution = 3.63 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= 0.009 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 9271 2.51 5 N 2245 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14081 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" 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: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2778 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2729 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2685 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Unusual residues: {'DD9': 1, 'HEX': 5, 'HP6': 3, 'NAG': 1, 'UND': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 97 Unusual residues: {'DD9': 2, 'HEX': 1, 'HP6': 1, 'NAG': 1, 'NBU': 2, 'UND': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 78 Unusual residues: {'D10': 2, 'DD9': 1, 'HEX': 3, 'NAG': 1, 'NBU': 3} Inner-chain residues flagged as termini: ['pdbres="GLY B 503 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 48 Unusual residues: {'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Unusual residues: {'D10': 1, 'HEX': 2, 'NAG': 1, 'NBU': 1, 'OCT': 2, 'UND': 1} Inner-chain residues flagged as termini: ['pdbres="GLY E 502 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.27, per 1000 atoms: 0.66 Number of scatterers: 14081 At special positions: 0 Unit cell: (102.09, 127.82, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 2464 8.00 N 2245 7.00 C 9271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, 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 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 38 " " NAG B 504 " - " ASN B 38 " " NAG C 502 " - " ASN C 38 " " NAG D 502 " - " ASN D 38 " " NAG E 503 " - " ASN E 220 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 29 sheets defined 41.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.705A pdb=" N SER D 22 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY D 23 " --> pdb=" O ARG D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 23' Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.744A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.711A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 243 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 272 Processing helix chain 'D' and resid 281 through 310 removed outlier: 4.007A pdb=" N ILE D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 417 removed outlier: 3.647A pdb=" N ILE D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.684A pdb=" N SER A 22 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.557A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.782A pdb=" N SER A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 271 removed outlier: 3.946A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 282 through 310 removed outlier: 3.937A pdb=" N TRP A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 418 Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.845A pdb=" N SER B 22 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.581A pdb=" N SER B 92 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.020A pdb=" N ASP B 148 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 220 through 243 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 272 removed outlier: 3.595A pdb=" N LEU B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.833A pdb=" N ILE B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 418 Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 10 through 18 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.698A pdb=" N SER C 22 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 23 " --> pdb=" O ARG C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.823A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.935A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 243 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 273 Processing helix chain 'C' and resid 281 through 310 removed outlier: 3.592A pdb=" N ILE C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 417 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 35 through 43 Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.572A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 109 through 116 removed outlier: 4.146A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 269 removed outlier: 4.142A pdb=" N ASN E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 296 Proline residue: E 278 - end of helix Processing helix chain 'E' and resid 305 through 333 Processing helix chain 'E' and resid 447 through 475 removed outlier: 3.704A pdb=" N ILE E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.621A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 40 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 169 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.589A pdb=" N THR D 133 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS D 107 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AA5, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.767A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.569A pdb=" N GLY D 205 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.508A pdb=" N LEU A 83 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 65 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 40 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.508A pdb=" N LEU A 83 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 65 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 40 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N GLN A 177 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 43 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.573A pdb=" N ASP A 57 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.794A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS A 215 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU A 192 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLU A 217 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LYS A 190 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 38 removed outlier: 5.798A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.746A pdb=" N SER B 40 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 45 Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.715A pdb=" N HIS B 107 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.523A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 200 through 202 Processing sheet with id=AC1, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.661A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 40 " --> pdb=" O GLN C 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AC3, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.584A pdb=" N HIS C 107 " --> pdb=" O THR C 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AC5, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.548A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.693A pdb=" N GLY C 205 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 141 through 143 removed outlier: 3.557A pdb=" N TRP E 89 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 66 through 69 Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AD1, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.740A pdb=" N ARG E 241 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.755A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY E 229 " --> pdb=" O TYR E 225 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1881 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: 4.90 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3698 1.33 - 1.46: 4026 1.46 - 1.59: 6486 1.59 - 1.72: 0 1.72 - 1.85: 170 Bond restraints: 14380 Sorted by residual: bond pdb=" N THR D 208 " pdb=" CA THR D 208 " ideal model delta sigma weight residual 1.454 1.499 -0.044 1.27e-02 6.20e+03 1.22e+01 bond pdb=" N PHE D 207 " pdb=" CA PHE D 207 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" N GLY C 501 " pdb=" CA GLY C 501 " ideal model delta sigma weight residual 1.451 1.503 -0.052 1.60e-02 3.91e+03 1.06e+01 bond pdb=" N ALA B 272 " pdb=" CA ALA B 272 " ideal model delta sigma weight residual 1.462 1.502 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N GLY A 501 " pdb=" CA GLY A 501 " ideal model delta sigma weight residual 1.451 1.503 -0.052 1.60e-02 3.91e+03 1.05e+01 ... (remaining 14375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18706 1.84 - 3.68: 530 3.68 - 5.52: 96 5.52 - 7.36: 17 7.36 - 9.20: 6 Bond angle restraints: 19355 Sorted by residual: angle pdb=" N MET B 246 " pdb=" CA MET B 246 " pdb=" C MET B 246 " ideal model delta sigma weight residual 111.28 102.08 9.20 1.09e+00 8.42e-01 7.12e+01 angle pdb=" N ILE B 244 " pdb=" CA ILE B 244 " pdb=" C ILE B 244 " ideal model delta sigma weight residual 108.44 99.53 8.91 1.55e+00 4.16e-01 3.31e+01 angle pdb=" N ALA B 272 " pdb=" CA ALA B 272 " pdb=" C ALA B 272 " ideal model delta sigma weight residual 110.70 118.86 -8.16 1.55e+00 4.16e-01 2.77e+01 angle pdb=" N CYS E 221 " pdb=" CA CYS E 221 " pdb=" C CYS E 221 " ideal model delta sigma weight residual 113.19 104.97 8.22 1.58e+00 4.01e-01 2.70e+01 angle pdb=" CA ILE B 244 " pdb=" C ILE B 244 " pdb=" O ILE B 244 " ideal model delta sigma weight residual 121.45 116.77 4.68 1.00e+00 1.00e+00 2.19e+01 ... (remaining 19350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8045 17.98 - 35.95: 508 35.95 - 53.93: 89 53.93 - 71.91: 17 71.91 - 89.89: 6 Dihedral angle restraints: 8665 sinusoidal: 3693 harmonic: 4972 Sorted by residual: dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 49.85 43.15 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 52.96 40.04 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 54.48 38.52 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 8662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1997 0.095 - 0.190: 127 0.190 - 0.285: 13 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 2141 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 38 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2138 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A 502 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 504 " -0.337 2.00e-02 2.50e+03 2.91e-01 1.05e+03 pdb=" C7 NAG B 504 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 504 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B 504 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG B 504 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG C 502 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " -0.195 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.94: 1 1.94 - 2.68: 274 2.68 - 3.42: 19587 3.42 - 4.16: 31379 4.16 - 4.90: 57800 Nonbonded interactions: 109041 Sorted by model distance: nonbonded pdb=" CD2 LEU D 261 " pdb=" CE1 PHE E 282 " model vdw 1.194 3.760 nonbonded pdb=" CD2 LEU D 261 " pdb=" CD1 PHE E 282 " model vdw 2.150 3.760 nonbonded pdb=" CE1 PHE A 159 " pdb=" N GLY A 501 " model vdw 2.163 3.420 nonbonded pdb=" CE1 PHE B 159 " pdb=" N GLY B 503 " model vdw 2.165 3.420 nonbonded pdb=" CE2 TYR E 231 " pdb=" N GLY E 502 " model vdw 2.177 3.420 ... (remaining 109036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 308 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me 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: 1.290 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 35.010 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14380 Z= 0.265 Angle : 0.733 9.200 19355 Z= 0.419 Chirality : 0.051 0.475 2141 Planarity : 0.012 0.295 2394 Dihedral : 11.886 89.887 5413 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.37 % Favored : 93.45 % Rotamer: Outliers : 1.52 % Allowed : 0.93 % Favored : 97.55 % 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: -0.87 (0.22), residues: 1664 helix: 2.47 (0.22), residues: 573 sheet: -2.68 (0.27), residues: 335 loop : -2.05 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP B 94 HIS 0.003 0.000 HIS D 201 PHE 0.023 0.001 PHE E 266 TYR 0.014 0.001 TYR D 301 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 411 MET cc_start: 0.7190 (tpp) cc_final: 0.6775 (mtt) REVERT: A 75 TYR cc_start: 0.8363 (p90) cc_final: 0.8153 (p90) REVERT: A 266 GLN cc_start: 0.7311 (mm110) cc_final: 0.7031 (mt0) REVERT: C 113 THR cc_start: 0.7933 (m) cc_final: 0.7713 (m) REVERT: E 133 ASP cc_start: 0.7650 (p0) cc_final: 0.7339 (p0) REVERT: E 152 SER cc_start: 0.8353 (p) cc_final: 0.7997 (p) outliers start: 23 outliers final: 8 residues processed: 303 average time/residue: 0.2445 time to fit residues: 111.1585 Evaluate side-chains 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 63 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14380 Z= 0.198 Angle : 0.676 9.322 19355 Z= 0.338 Chirality : 0.047 0.572 2141 Planarity : 0.004 0.035 2394 Dihedral : 7.332 86.721 2136 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 2.25 % Allowed : 9.20 % Favored : 88.55 % 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: -0.72 (0.21), residues: 1664 helix: 2.73 (0.22), residues: 573 sheet: -2.41 (0.27), residues: 355 loop : -2.17 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.003 0.001 HIS C 201 PHE 0.012 0.001 PHE D 412 TYR 0.011 0.001 TYR D 413 ARG 0.007 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 MET cc_start: 0.8824 (tpp) cc_final: 0.8483 (tpp) REVERT: D 219 GLN cc_start: 0.8307 (mt0) cc_final: 0.8015 (mt0) REVERT: D 226 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6111 (mm110) REVERT: A 266 GLN cc_start: 0.7360 (mm110) cc_final: 0.7067 (mt0) REVERT: C 93 ILE cc_start: 0.8854 (mm) cc_final: 0.8644 (mt) REVERT: E 133 ASP cc_start: 0.7674 (p0) cc_final: 0.7470 (p0) REVERT: E 152 SER cc_start: 0.8399 (p) cc_final: 0.8155 (p) outliers start: 34 outliers final: 24 residues processed: 272 average time/residue: 0.2390 time to fit residues: 98.2971 Evaluate side-chains 255 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 151 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14380 Z= 0.199 Angle : 0.611 8.750 19355 Z= 0.308 Chirality : 0.045 0.603 2141 Planarity : 0.004 0.033 2394 Dihedral : 6.245 85.686 2126 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 3.31 % Allowed : 11.25 % Favored : 85.44 % 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: 1664 helix: 2.83 (0.22), residues: 579 sheet: -2.25 (0.26), residues: 370 loop : -2.10 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.002 0.001 HIS C 109 PHE 0.012 0.001 PHE A 63 TYR 0.014 0.001 TYR B 413 ARG 0.006 0.000 ARG E 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8189 (m) cc_final: 0.7916 (m) REVERT: D 219 GLN cc_start: 0.8356 (mt0) cc_final: 0.8089 (mt0) REVERT: D 226 GLN cc_start: 0.6597 (mm-40) cc_final: 0.6363 (mm110) REVERT: A 89 MET cc_start: 0.8071 (ppp) cc_final: 0.7827 (ppp) REVERT: E 152 SER cc_start: 0.8495 (p) cc_final: 0.8267 (p) REVERT: E 459 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7016 (t80) outliers start: 50 outliers final: 34 residues processed: 269 average time/residue: 0.2328 time to fit residues: 95.7302 Evaluate side-chains 262 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14380 Z= 0.208 Angle : 0.610 8.585 19355 Z= 0.305 Chirality : 0.044 0.559 2141 Planarity : 0.004 0.036 2394 Dihedral : 6.187 85.046 2126 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 3.18 % Allowed : 13.70 % Favored : 83.12 % 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 (0.22), residues: 1664 helix: 2.87 (0.22), residues: 578 sheet: -2.04 (0.27), residues: 355 loop : -2.11 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 286 HIS 0.002 0.001 HIS C 109 PHE 0.013 0.001 PHE A 63 TYR 0.025 0.001 TYR B 301 ARG 0.005 0.000 ARG E 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8147 (m) cc_final: 0.7857 (m) REVERT: D 219 GLN cc_start: 0.8371 (mt0) cc_final: 0.8088 (mt0) REVERT: A 283 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7573 (tt) REVERT: C 299 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (mp) REVERT: E 152 SER cc_start: 0.8517 (p) cc_final: 0.8293 (p) outliers start: 48 outliers final: 36 residues processed: 262 average time/residue: 0.2373 time to fit residues: 95.5774 Evaluate side-chains 259 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 111 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14380 Z= 0.297 Angle : 0.640 9.906 19355 Z= 0.322 Chirality : 0.045 0.546 2141 Planarity : 0.004 0.041 2394 Dihedral : 6.391 81.115 2126 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer: Outliers : 4.43 % Allowed : 13.83 % Favored : 81.73 % 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 (0.22), residues: 1664 helix: 2.89 (0.22), residues: 572 sheet: -2.02 (0.27), residues: 362 loop : -2.09 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 267 HIS 0.003 0.001 HIS C 201 PHE 0.017 0.002 PHE B 293 TYR 0.017 0.001 TYR E 325 ARG 0.007 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8225 (m) cc_final: 0.7942 (m) REVERT: D 219 GLN cc_start: 0.8397 (mt0) cc_final: 0.8122 (mt0) REVERT: A 89 MET cc_start: 0.8171 (ppp) cc_final: 0.7958 (ppp) REVERT: A 287 MET cc_start: 0.7935 (ttm) cc_final: 0.7636 (ttm) REVERT: C 299 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8361 (mp) REVERT: E 152 SER cc_start: 0.8586 (p) cc_final: 0.8333 (p) REVERT: E 465 PHE cc_start: 0.8225 (t80) cc_final: 0.8024 (t80) outliers start: 67 outliers final: 45 residues processed: 260 average time/residue: 0.2834 time to fit residues: 113.0606 Evaluate side-chains 262 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14380 Z= 0.231 Angle : 0.621 9.301 19355 Z= 0.309 Chirality : 0.044 0.530 2141 Planarity : 0.004 0.037 2394 Dihedral : 6.269 71.108 2126 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 4.10 % Allowed : 14.82 % Favored : 81.07 % 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: -0.37 (0.22), residues: 1664 helix: 2.92 (0.22), residues: 572 sheet: -1.99 (0.27), residues: 369 loop : -1.97 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.002 0.001 HIS A 109 PHE 0.017 0.001 PHE A 63 TYR 0.016 0.001 TYR E 325 ARG 0.004 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8142 (m) cc_final: 0.7851 (m) REVERT: D 219 GLN cc_start: 0.8367 (mt0) cc_final: 0.8149 (mt0) REVERT: A 89 MET cc_start: 0.8144 (ppp) cc_final: 0.7921 (ppp) REVERT: A 415 ILE cc_start: 0.8740 (tp) cc_final: 0.8539 (tp) REVERT: C 299 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8335 (mp) REVERT: E 152 SER cc_start: 0.8521 (p) cc_final: 0.8251 (p) REVERT: E 465 PHE cc_start: 0.8224 (t80) cc_final: 0.8013 (t80) outliers start: 62 outliers final: 48 residues processed: 257 average time/residue: 0.2353 time to fit residues: 92.6627 Evaluate side-chains 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14380 Z= 0.209 Angle : 0.613 9.126 19355 Z= 0.305 Chirality : 0.044 0.521 2141 Planarity : 0.003 0.035 2394 Dihedral : 6.217 59.797 2125 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.35 % Rotamer: Outliers : 4.30 % Allowed : 15.62 % Favored : 80.08 % 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: -0.31 (0.22), residues: 1664 helix: 2.86 (0.22), residues: 578 sheet: -1.86 (0.27), residues: 361 loop : -1.95 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 414 HIS 0.002 0.001 HIS C 107 PHE 0.016 0.001 PHE A 63 TYR 0.014 0.001 TYR E 325 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8188 (m) cc_final: 0.7919 (m) REVERT: D 219 GLN cc_start: 0.8361 (mt0) cc_final: 0.8160 (mt0) REVERT: A 89 MET cc_start: 0.8175 (ppp) cc_final: 0.7951 (ppp) REVERT: A 190 LYS cc_start: 0.8461 (mttm) cc_final: 0.8171 (mmmm) REVERT: A 227 MET cc_start: 0.6720 (ttm) cc_final: 0.6442 (ttt) REVERT: A 415 ILE cc_start: 0.8733 (tp) cc_final: 0.8533 (tp) REVERT: C 299 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8325 (mp) REVERT: E 152 SER cc_start: 0.8617 (p) cc_final: 0.8387 (p) REVERT: E 465 PHE cc_start: 0.8138 (t80) cc_final: 0.7889 (t80) outliers start: 65 outliers final: 53 residues processed: 255 average time/residue: 0.2314 time to fit residues: 91.0375 Evaluate side-chains 270 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 0.0170 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14380 Z= 0.264 Angle : 0.638 9.401 19355 Z= 0.316 Chirality : 0.044 0.523 2141 Planarity : 0.004 0.035 2394 Dihedral : 6.410 59.699 2125 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 4.24 % Allowed : 16.08 % Favored : 79.68 % 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: -0.33 (0.22), residues: 1664 helix: 2.80 (0.22), residues: 578 sheet: -1.83 (0.28), residues: 361 loop : -1.95 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.002 0.001 HIS C 201 PHE 0.017 0.001 PHE A 63 TYR 0.015 0.001 TYR E 252 ARG 0.004 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8206 (m) cc_final: 0.7930 (m) REVERT: D 171 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: A 89 MET cc_start: 0.8232 (ppp) cc_final: 0.8019 (ppp) REVERT: A 227 MET cc_start: 0.6771 (ttm) cc_final: 0.6456 (ttt) REVERT: A 287 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7460 (mmm) REVERT: A 415 ILE cc_start: 0.8733 (tp) cc_final: 0.8522 (tp) REVERT: B 147 MET cc_start: 0.7778 (mpp) cc_final: 0.7484 (mtm) REVERT: C 299 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 39 ASN cc_start: 0.9007 (m-40) cc_final: 0.8767 (m-40) REVERT: E 152 SER cc_start: 0.8671 (p) cc_final: 0.8453 (p) REVERT: E 465 PHE cc_start: 0.8172 (t80) cc_final: 0.7968 (t80) outliers start: 64 outliers final: 51 residues processed: 251 average time/residue: 0.2285 time to fit residues: 88.4723 Evaluate side-chains 269 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 135 optimal weight: 0.0870 chunk 141 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN E 138 ASN E 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14380 Z= 0.154 Angle : 0.606 10.400 19355 Z= 0.298 Chirality : 0.043 0.498 2141 Planarity : 0.003 0.031 2394 Dihedral : 6.073 55.944 2125 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 2.65 % Allowed : 18.07 % Favored : 79.29 % 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: -0.28 (0.22), residues: 1664 helix: 2.84 (0.22), residues: 579 sheet: -1.76 (0.27), residues: 369 loop : -1.94 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 414 HIS 0.002 0.000 HIS A 215 PHE 0.015 0.001 PHE E 100 TYR 0.013 0.001 TYR C 128 ARG 0.004 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8124 (m) cc_final: 0.7877 (m) REVERT: A 227 MET cc_start: 0.6792 (ttm) cc_final: 0.6421 (ttt) REVERT: A 287 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7241 (mmm) REVERT: A 415 ILE cc_start: 0.8727 (tp) cc_final: 0.8514 (tp) REVERT: B 147 MET cc_start: 0.7773 (mpp) cc_final: 0.7441 (mtm) REVERT: C 299 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8265 (mp) REVERT: E 39 ASN cc_start: 0.9004 (m-40) cc_final: 0.8775 (m-40) REVERT: E 152 SER cc_start: 0.8506 (p) cc_final: 0.8233 (p) REVERT: E 465 PHE cc_start: 0.8039 (t80) cc_final: 0.7812 (t80) outliers start: 40 outliers final: 30 residues processed: 252 average time/residue: 0.2273 time to fit residues: 87.9139 Evaluate side-chains 245 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14380 Z= 0.184 Angle : 0.630 10.511 19355 Z= 0.305 Chirality : 0.043 0.499 2141 Planarity : 0.003 0.030 2394 Dihedral : 6.018 55.940 2125 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 2.58 % Allowed : 18.40 % Favored : 79.02 % 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: -0.26 (0.22), residues: 1664 helix: 2.78 (0.22), residues: 584 sheet: -1.69 (0.27), residues: 359 loop : -1.93 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.001 0.001 HIS C 107 PHE 0.012 0.001 PHE E 100 TYR 0.012 0.001 TYR D 128 ARG 0.003 0.000 ARG A 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8200 (m) cc_final: 0.7947 (m) REVERT: A 227 MET cc_start: 0.6768 (ttm) cc_final: 0.6314 (ttt) REVERT: A 287 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7275 (mmm) REVERT: A 415 ILE cc_start: 0.8749 (tp) cc_final: 0.8524 (tp) REVERT: B 147 MET cc_start: 0.7813 (mpp) cc_final: 0.7442 (mtm) REVERT: C 299 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8256 (mp) REVERT: E 39 ASN cc_start: 0.9007 (m-40) cc_final: 0.8758 (m-40) REVERT: E 152 SER cc_start: 0.8488 (p) cc_final: 0.8249 (p) REVERT: E 465 PHE cc_start: 0.8054 (t80) cc_final: 0.7851 (t80) outliers start: 39 outliers final: 33 residues processed: 245 average time/residue: 0.2375 time to fit residues: 89.3680 Evaluate side-chains 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 132 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118047 restraints weight = 19835.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121027 restraints weight = 12379.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122929 restraints weight = 9062.302| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14380 Z= 0.156 Angle : 0.611 10.531 19355 Z= 0.296 Chirality : 0.043 0.486 2141 Planarity : 0.003 0.030 2394 Dihedral : 5.824 58.280 2125 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 2.71 % Allowed : 18.53 % Favored : 78.76 % 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: -0.09 (0.22), residues: 1664 helix: 2.98 (0.22), residues: 568 sheet: -1.56 (0.28), residues: 359 loop : -1.80 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.001 0.000 HIS B 109 PHE 0.012 0.001 PHE A 63 TYR 0.013 0.001 TYR C 128 ARG 0.003 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2959.25 seconds wall clock time: 54 minutes 51.69 seconds (3291.69 seconds total)