Starting phenix.real_space_refine on Sat Aug 23 22:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn5_27555/08_2025/8dn5_27555_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn5_27555/08_2025/8dn5_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_27555/08_2025/8dn5_27555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn5_27555/08_2025/8dn5_27555.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn5_27555/08_2025/8dn5_27555_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn5_27555/08_2025/8dn5_27555_trim.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.04, per 1000 atoms: 0.22 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: 0.98 Conformation dependent library (CDL) restraints added in 458.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 1.87 Time building geometry restraints manager: 1.23 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- 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 : 0.006 0.449 14398 Z= 0.516 Angle : 0.744 9.200 19390 Z= 0.421 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 : 14.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 399 TYR 0.014 0.001 TYR D 301 PHE 0.023 0.001 PHE E 266 TRP 0.055 0.001 TRP B 94 HIS 0.003 0.000 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00410 (14380) covalent geometry : angle 0.73297 (19355) SS BOND : bond 0.00496 ( 10) SS BOND : angle 1.64440 ( 20) hydrogen bonds : bond 0.17728 ( 627) hydrogen bonds : angle 6.84377 ( 1881) Misc. bond : bond 0.31439 ( 3) link_NAG-ASN : bond 0.00694 ( 5) link_NAG-ASN : angle 4.33240 ( 15) *********************** 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 : 0.382 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: 0.0844 time to fit residues: 39.4747 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 : 0.498 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119148 restraints weight = 19858.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122119 restraints weight = 12307.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124034 restraints weight = 8959.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125310 restraints weight = 7319.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125830 restraints weight = 6412.246| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14398 Z= 0.140 Angle : 0.712 22.491 19390 Z= 0.346 Chirality : 0.047 0.602 2141 Planarity : 0.004 0.035 2394 Dihedral : 7.331 87.233 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 : 2.38 % Allowed : 8.93 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1664 helix: 2.74 (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 ARG 0.007 0.000 ARG A 271 TYR 0.011 0.001 TYR D 413 PHE 0.013 0.001 PHE E 282 TRP 0.018 0.001 TRP B 94 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00312 (14380) covalent geometry : angle 0.67910 (19355) SS BOND : bond 0.00487 ( 10) SS BOND : angle 1.87439 ( 20) hydrogen bonds : bond 0.04449 ( 627) hydrogen bonds : angle 5.01431 ( 1881) Misc. bond : bond 0.00521 ( 3) link_NAG-ASN : bond 0.00712 ( 5) link_NAG-ASN : angle 7.48156 ( 15) *********************** 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 284 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.8874 (mmt) cc_final: 0.8621 (mmt) REVERT: D 219 GLN cc_start: 0.8519 (mt0) cc_final: 0.8152 (mt0) REVERT: D 226 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6555 (mm110) REVERT: A 287 MET cc_start: 0.7554 (mmm) cc_final: 0.7215 (ttm) REVERT: E 152 SER cc_start: 0.8803 (p) cc_final: 0.8539 (p) outliers start: 36 outliers final: 24 residues processed: 273 average time/residue: 0.0944 time to fit residues: 39.3752 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 : 0.403 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120960 restraints weight = 19976.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123962 restraints weight = 12243.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126014 restraints weight = 8858.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127092 restraints weight = 7187.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128090 restraints weight = 6349.835| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14398 Z= 0.114 Angle : 0.615 15.465 19390 Z= 0.304 Chirality : 0.045 0.599 2141 Planarity : 0.004 0.031 2394 Dihedral : 6.114 85.813 2126 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 2.91 % Allowed : 11.32 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.22), residues: 1664 helix: 2.84 (0.22), residues: 579 sheet: -2.19 (0.27), residues: 362 loop : -2.09 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 174 TYR 0.013 0.001 TYR E 325 PHE 0.011 0.001 PHE D 306 TRP 0.009 0.001 TRP B 94 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00246 (14380) covalent geometry : angle 0.59739 (19355) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.36661 ( 20) hydrogen bonds : bond 0.03751 ( 627) hydrogen bonds : angle 4.55094 ( 1881) Misc. bond : bond 0.00024 ( 3) link_NAG-ASN : bond 0.01140 ( 5) link_NAG-ASN : angle 5.01563 ( 15) *********************** 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 297 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 75 TYR cc_start: 0.7827 (p90) cc_final: 0.7556 (p90) REVERT: D 113 THR cc_start: 0.8424 (m) cc_final: 0.8121 (m) REVERT: D 219 GLN cc_start: 0.8523 (mt0) cc_final: 0.8142 (mt0) REVERT: D 226 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6629 (mm110) REVERT: D 411 MET cc_start: 0.7456 (tpp) cc_final: 0.7207 (tpp) REVERT: A 89 MET cc_start: 0.8248 (ppp) cc_final: 0.8003 (ppp) REVERT: A 279 TYR cc_start: 0.8843 (p90) cc_final: 0.7943 (p90) REVERT: E 152 SER cc_start: 0.8818 (p) cc_final: 0.8553 (p) REVERT: E 459 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7038 (t80) outliers start: 44 outliers final: 29 residues processed: 276 average time/residue: 0.0962 time to fit residues: 41.5731 Evaluate side-chains 261 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 273 SER 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 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL 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 43 ILE 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 299 LEU Chi-restraints excluded: chain C residue 402 PHE 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 156 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 125 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118103 restraints weight = 20035.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121117 restraints weight = 12353.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123096 restraints weight = 8984.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124299 restraints weight = 7323.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124824 restraints weight = 6451.859| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14398 Z= 0.124 Angle : 0.612 13.500 19390 Z= 0.302 Chirality : 0.044 0.543 2141 Planarity : 0.003 0.032 2394 Dihedral : 5.964 86.593 2126 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 3.44 % Allowed : 12.97 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1664 helix: 2.89 (0.22), residues: 578 sheet: -2.01 (0.28), residues: 347 loop : -2.07 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 276 TYR 0.025 0.001 TYR B 301 PHE 0.012 0.001 PHE A 44 TRP 0.007 0.001 TRP B 286 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00281 (14380) covalent geometry : angle 0.59976 (19355) SS BOND : bond 0.00337 ( 10) SS BOND : angle 1.24069 ( 20) hydrogen bonds : bond 0.03647 ( 627) hydrogen bonds : angle 4.40027 ( 1881) Misc. bond : bond 0.00032 ( 3) link_NAG-ASN : bond 0.00928 ( 5) link_NAG-ASN : angle 4.31846 ( 15) *********************** 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 279 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.577 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: 0.8359 (m) cc_final: 0.8056 (m) REVERT: D 219 GLN cc_start: 0.8551 (mt0) cc_final: 0.8213 (mt0) REVERT: D 226 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6597 (mm110) REVERT: D 411 MET cc_start: 0.7562 (tpp) cc_final: 0.7287 (tpp) REVERT: A 279 TYR cc_start: 0.8882 (p90) cc_final: 0.7947 (p90) outliers start: 52 outliers final: 36 residues processed: 258 average time/residue: 0.1007 time to fit residues: 40.9250 Evaluate side-chains 256 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 55 THR 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 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 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU 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 323 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 105 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 147 optimal weight: 0.3980 chunk 58 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN C 150 GLN E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117728 restraints weight = 20125.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120738 restraints weight = 12395.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122721 restraints weight = 9021.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123914 restraints weight = 7377.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124749 restraints weight = 6516.374| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14398 Z= 0.120 Angle : 0.591 12.858 19390 Z= 0.292 Chirality : 0.043 0.522 2141 Planarity : 0.003 0.033 2394 Dihedral : 5.777 82.357 2126 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 3.71 % Allowed : 13.96 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1664 helix: 3.00 (0.22), residues: 572 sheet: -2.01 (0.27), residues: 370 loop : -1.93 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.017 0.001 TYR E 325 PHE 0.012 0.001 PHE A 63 TRP 0.007 0.001 TRP B 286 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00272 (14380) covalent geometry : angle 0.57979 (19355) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.17607 ( 20) hydrogen bonds : bond 0.03545 ( 627) hydrogen bonds : angle 4.30741 ( 1881) Misc. bond : bond 0.00020 ( 3) link_NAG-ASN : bond 0.00919 ( 5) link_NAG-ASN : angle 3.97556 ( 15) *********************** 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 282 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8260 (m) cc_final: 0.7965 (m) REVERT: D 219 GLN cc_start: 0.8483 (mt0) cc_final: 0.8166 (mt0) REVERT: D 411 MET cc_start: 0.7572 (tpp) cc_final: 0.7308 (tpp) REVERT: A 89 MET cc_start: 0.8228 (ppp) cc_final: 0.8028 (ppp) REVERT: A 217 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 279 TYR cc_start: 0.8877 (p90) cc_final: 0.8598 (p90) REVERT: C 97 ASP cc_start: 0.8542 (p0) cc_final: 0.8328 (p0) REVERT: C 110 GLU cc_start: 0.7025 (pm20) cc_final: 0.6707 (pm20) outliers start: 56 outliers final: 38 residues processed: 260 average time/residue: 0.1080 time to fit residues: 44.0066 Evaluate side-chains 258 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain D residue 188 ILE 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 274 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU 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 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU 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 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 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR 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 96 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 38 optimal weight: 0.0370 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119146 restraints weight = 19892.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122188 restraints weight = 12305.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124052 restraints weight = 8933.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125423 restraints weight = 7308.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126015 restraints weight = 6415.552| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14398 Z= 0.109 Angle : 0.591 12.434 19390 Z= 0.290 Chirality : 0.043 0.510 2141 Planarity : 0.003 0.028 2394 Dihedral : 5.591 76.356 2125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 3.51 % Allowed : 14.96 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.22), residues: 1664 helix: 2.96 (0.22), residues: 574 sheet: -1.88 (0.27), residues: 362 loop : -1.88 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.013 0.001 TYR E 325 PHE 0.012 0.001 PHE A 63 TRP 0.006 0.001 TRP B 286 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00243 (14380) covalent geometry : angle 0.58123 (19355) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.14355 ( 20) hydrogen bonds : bond 0.03385 ( 627) hydrogen bonds : angle 4.19898 ( 1881) Misc. bond : bond 0.00019 ( 3) link_NAG-ASN : bond 0.00922 ( 5) link_NAG-ASN : angle 3.77154 ( 15) *********************** 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 288 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ILE cc_start: 0.8668 (mm) cc_final: 0.8391 (mm) REVERT: D 113 THR cc_start: 0.8306 (m) cc_final: 0.8019 (m) REVERT: D 219 GLN cc_start: 0.8478 (mt0) cc_final: 0.8173 (mt0) REVERT: D 411 MET cc_start: 0.7491 (tpp) cc_final: 0.7246 (tpp) REVERT: A 89 MET cc_start: 0.8212 (ppp) cc_final: 0.7947 (ppp) REVERT: A 141 ASP cc_start: 0.8310 (t70) cc_final: 0.7902 (t0) REVERT: A 217 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 279 TYR cc_start: 0.8832 (p90) cc_final: 0.8593 (p90) REVERT: A 287 MET cc_start: 0.7711 (ttm) cc_final: 0.7384 (ttm) REVERT: C 97 ASP cc_start: 0.8541 (p0) cc_final: 0.8334 (p0) outliers start: 53 outliers final: 42 residues processed: 264 average time/residue: 0.0835 time to fit residues: 34.4994 Evaluate side-chains 263 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 211 GLU 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 274 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU 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 195 LEU 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 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 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 283 ILE Chi-restraints excluded: chain C residue 285 ILE 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 323 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 23 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 171 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109806 restraints weight = 20413.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112552 restraints weight = 13088.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114345 restraints weight = 9751.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115485 restraints weight = 8058.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116038 restraints weight = 7178.038| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14398 Z= 0.260 Angle : 0.715 12.799 19390 Z= 0.357 Chirality : 0.047 0.541 2141 Planarity : 0.004 0.039 2394 Dihedral : 6.650 72.994 2125 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.17 % Allowed : 15.62 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.21), residues: 1664 helix: 2.55 (0.22), residues: 589 sheet: -1.79 (0.28), residues: 349 loop : -2.08 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 271 TYR 0.021 0.002 TYR A 301 PHE 0.027 0.002 PHE B 293 TRP 0.016 0.001 TRP E 267 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00623 (14380) covalent geometry : angle 0.70560 (19355) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.28488 ( 20) hydrogen bonds : bond 0.04553 ( 627) hydrogen bonds : angle 4.56247 ( 1881) Misc. bond : bond 0.00039 ( 3) link_NAG-ASN : bond 0.00923 ( 5) link_NAG-ASN : angle 3.99221 ( 15) *********************** 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 286 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8495 (m) cc_final: 0.8226 (m) REVERT: D 219 GLN cc_start: 0.8573 (mt0) cc_final: 0.8217 (mt0) REVERT: D 411 MET cc_start: 0.7473 (tpp) cc_final: 0.7069 (tpp) REVERT: A 89 MET cc_start: 0.8373 (ppp) cc_final: 0.8062 (ppp) REVERT: A 113 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8580 (m) REVERT: A 287 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7543 (mmm) REVERT: B 226 GLN cc_start: 0.6896 (tm-30) cc_final: 0.6405 (tm-30) REVERT: E 95 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8530 (mtmm) REVERT: E 152 SER cc_start: 0.9004 (p) cc_final: 0.8787 (p) REVERT: E 214 GLU cc_start: 0.7606 (pp20) cc_final: 0.7197 (pp20) REVERT: E 465 PHE cc_start: 0.8332 (t80) cc_final: 0.7996 (t80) outliers start: 63 outliers final: 43 residues processed: 259 average time/residue: 0.0944 time to fit residues: 37.9729 Evaluate side-chains 263 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 113 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 227 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 ILE 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 C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114254 restraints weight = 19989.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117143 restraints weight = 12545.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119077 restraints weight = 9245.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120320 restraints weight = 7583.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120857 restraints weight = 6687.562| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14398 Z= 0.132 Angle : 0.636 12.480 19390 Z= 0.312 Chirality : 0.044 0.516 2141 Planarity : 0.003 0.033 2394 Dihedral : 6.348 58.016 2125 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.81 % Favored : 95.07 % Rotamer: Outliers : 3.57 % Allowed : 16.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1664 helix: 2.81 (0.22), residues: 584 sheet: -1.88 (0.27), residues: 369 loop : -1.84 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.014 0.001 TYR A 301 PHE 0.018 0.001 PHE A 63 TRP 0.018 0.001 TRP C 414 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00301 (14380) covalent geometry : angle 0.62678 (19355) SS BOND : bond 0.00324 ( 10) SS BOND : angle 1.09418 ( 20) hydrogen bonds : bond 0.03820 ( 627) hydrogen bonds : angle 4.33019 ( 1881) Misc. bond : bond 0.00025 ( 3) link_NAG-ASN : bond 0.01016 ( 5) link_NAG-ASN : angle 3.85023 ( 15) *********************** 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 280 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8341 (m) cc_final: 0.8023 (m) REVERT: D 219 GLN cc_start: 0.8466 (mt0) cc_final: 0.8210 (mt0) REVERT: A 89 MET cc_start: 0.8270 (ppp) cc_final: 0.7994 (ppp) REVERT: A 279 TYR cc_start: 0.8863 (p90) cc_final: 0.8173 (p90) REVERT: A 287 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7390 (mmm) REVERT: E 95 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8532 (mtmm) REVERT: E 152 SER cc_start: 0.8814 (p) cc_final: 0.8554 (p) REVERT: E 465 PHE cc_start: 0.8195 (t80) cc_final: 0.7888 (t80) outliers start: 54 outliers final: 44 residues processed: 254 average time/residue: 0.0821 time to fit residues: 32.7085 Evaluate side-chains 268 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 211 GLU 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 300 GLU 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 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 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 ILE 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 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 109 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR 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 107 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 120 optimal weight: 0.0060 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115048 restraints weight = 20120.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117936 restraints weight = 12581.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119891 restraints weight = 9282.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121143 restraints weight = 7601.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121698 restraints weight = 6689.906| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14398 Z= 0.128 Angle : 0.627 12.212 19390 Z= 0.306 Chirality : 0.044 0.505 2141 Planarity : 0.003 0.034 2394 Dihedral : 6.157 55.561 2125 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 3.18 % Allowed : 17.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1664 helix: 2.75 (0.22), residues: 590 sheet: -1.83 (0.27), residues: 367 loop : -1.83 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.013 0.001 TYR C 128 PHE 0.015 0.001 PHE A 63 TRP 0.013 0.001 TRP C 414 HIS 0.001 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00295 (14380) covalent geometry : angle 0.61778 (19355) SS BOND : bond 0.00314 ( 10) SS BOND : angle 1.10895 ( 20) hydrogen bonds : bond 0.03686 ( 627) hydrogen bonds : angle 4.25407 ( 1881) Misc. bond : bond 0.00027 ( 3) link_NAG-ASN : bond 0.00938 ( 5) link_NAG-ASN : angle 3.71087 ( 15) *********************** 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 273 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.522 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: 0.8323 (m) cc_final: 0.8035 (m) REVERT: D 219 GLN cc_start: 0.8455 (mt0) cc_final: 0.8218 (mt0) REVERT: A 89 MET cc_start: 0.8313 (ppp) cc_final: 0.8017 (ppp) REVERT: A 190 LYS cc_start: 0.8599 (mttm) cc_final: 0.8247 (mmmm) REVERT: A 279 TYR cc_start: 0.8863 (p90) cc_final: 0.8157 (p90) REVERT: E 95 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8535 (mtmm) REVERT: E 152 SER cc_start: 0.8758 (p) cc_final: 0.8497 (p) REVERT: E 465 PHE cc_start: 0.8181 (t80) cc_final: 0.7963 (t80) outliers start: 48 outliers final: 43 residues processed: 251 average time/residue: 0.0824 time to fit residues: 32.0733 Evaluate side-chains 261 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 211 GLU 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 227 MET Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU 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 274 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 ILE 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 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 323 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113145 restraints weight = 20155.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115941 restraints weight = 12733.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117886 restraints weight = 9414.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118977 restraints weight = 7715.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119495 restraints weight = 6854.370| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14398 Z= 0.168 Angle : 0.659 12.245 19390 Z= 0.322 Chirality : 0.045 0.514 2141 Planarity : 0.004 0.038 2394 Dihedral : 6.324 58.476 2125 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 2.98 % Allowed : 17.94 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1664 helix: 2.67 (0.22), residues: 590 sheet: -1.76 (0.27), residues: 360 loop : -1.84 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.014 0.001 TYR A 301 PHE 0.017 0.001 PHE A 63 TRP 0.014 0.001 TRP A 286 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00398 (14380) covalent geometry : angle 0.65086 (19355) SS BOND : bond 0.00325 ( 10) SS BOND : angle 1.13715 ( 20) hydrogen bonds : bond 0.03880 ( 627) hydrogen bonds : angle 4.30810 ( 1881) Misc. bond : bond 0.00028 ( 3) link_NAG-ASN : bond 0.00923 ( 5) link_NAG-ASN : angle 3.72585 ( 15) ********************** 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 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 THR cc_start: 0.8369 (m) cc_final: 0.8101 (m) REVERT: A 279 TYR cc_start: 0.8898 (p90) cc_final: 0.8238 (p90) REVERT: E 95 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8536 (mtmm) REVERT: E 152 SER cc_start: 0.8837 (p) cc_final: 0.8614 (p) REVERT: E 465 PHE cc_start: 0.8200 (t80) cc_final: 0.7992 (t80) outliers start: 45 outliers final: 41 residues processed: 246 average time/residue: 0.0864 time to fit residues: 32.7800 Evaluate side-chains 259 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU 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 227 MET Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU 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 274 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 93 ILE 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 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 E residue 72 ILE Chi-restraints excluded: chain E residue 261 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 151 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112670 restraints weight = 20049.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115440 restraints weight = 12734.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117278 restraints weight = 9480.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118291 restraints weight = 7843.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119175 restraints weight = 6993.688| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14398 Z= 0.168 Angle : 0.653 12.221 19390 Z= 0.320 Chirality : 0.045 0.512 2141 Planarity : 0.004 0.036 2394 Dihedral : 6.433 58.582 2125 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 3.18 % Allowed : 17.41 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1664 helix: 2.58 (0.22), residues: 596 sheet: -1.72 (0.28), residues: 351 loop : -1.85 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.015 0.001 TYR A 301 PHE 0.017 0.001 PHE A 63 TRP 0.013 0.001 TRP C 414 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00396 (14380) covalent geometry : angle 0.64428 (19355) SS BOND : bond 0.00311 ( 10) SS BOND : angle 1.12038 ( 20) hydrogen bonds : bond 0.03919 ( 627) hydrogen bonds : angle 4.32128 ( 1881) Misc. bond : bond 0.00034 ( 3) link_NAG-ASN : bond 0.00913 ( 5) link_NAG-ASN : angle 3.71972 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.73 seconds wall clock time: 35 minutes 7.30 seconds (2107.30 seconds total)