Starting phenix.real_space_refine on Sun Jul 21 02:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/07_2024/8tul_41624_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.268 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 14 5.21 5 S 65 5.16 5 C 8195 2.51 5 N 2150 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 262": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Time building chain proxies: 7.70, per 1000 atoms: 0.59 Number of scatterers: 13070 At special positions: 0 Unit cell: (106.24, 107.07, 140.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 14 11.99 O 2646 8.00 N 2150 7.00 C 8195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 68.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 219 Proline residue: A 209 - end of helix removed outlier: 3.607A pdb=" N ALA A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.633A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 219 Proline residue: B 209 - end of helix removed outlier: 3.607A pdb=" N ALA B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 219 Proline residue: C 209 - end of helix removed outlier: 3.607A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.027A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.755A pdb=" N GLY D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 219 Proline residue: D 209 - end of helix removed outlier: 3.607A pdb=" N ALA D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 359 removed outlier: 3.536A pdb=" N TYR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 219 Proline residue: E 209 - end of helix removed outlier: 3.608A pdb=" N ALA E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP E 273 " --> pdb=" O CYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102 removed outlier: 4.013A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 5.66 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: 3259 1.33 - 1.45: 2212 1.45 - 1.57: 7409 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13000 Sorted by residual: bond pdb=" C MET D 336 " pdb=" O MET D 336 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" C MET E 336 " pdb=" O MET E 336 " ideal model delta sigma weight residual 1.236 1.215 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" C MET C 336 " pdb=" O MET C 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET B 336 " pdb=" O MET B 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET A 336 " pdb=" O MET A 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.72e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 243 106.27 - 113.20: 7173 113.20 - 120.13: 4456 120.13 - 127.07: 5584 127.07 - 134.00: 99 Bond angle restraints: 17555 Sorted by residual: angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY B 353 " pdb=" CA GLY B 353 " pdb=" C GLY B 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY A 353 " pdb=" CA GLY A 353 " pdb=" C GLY A 353 " ideal model delta sigma weight residual 115.32 111.29 4.03 1.31e+00 5.83e-01 9.45e+00 angle pdb=" N GLY E 353 " pdb=" CA GLY E 353 " pdb=" C GLY E 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.30e+00 angle pdb=" N GLY D 353 " pdb=" CA GLY D 353 " pdb=" C GLY D 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.27e+00 ... (remaining 17550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6794 17.97 - 35.95: 823 35.95 - 53.92: 218 53.92 - 71.89: 50 71.89 - 89.87: 15 Dihedral angle restraints: 7900 sinusoidal: 3270 harmonic: 4630 Sorted by residual: dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " pdb=" CD GLU C 110 " pdb=" OE1 GLU C 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.84 -89.84 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1234 0.026 - 0.051: 495 0.051 - 0.077: 204 0.077 - 0.102: 51 0.102 - 0.128: 36 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2017 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO C 146 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 145 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.052 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 241 2.68 - 3.23: 11958 3.23 - 3.79: 20225 3.79 - 4.34: 29920 4.34 - 4.90: 48448 Nonbonded interactions: 110792 Sorted by model distance: nonbonded pdb="MG MG E 500 " pdb=" O HOH D 646 " model vdw 2.121 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH E 645 " model vdw 2.121 2.170 nonbonded pdb="MG MG D 500 " pdb=" O HOH C 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG C 501 " pdb=" O HOH B 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG B 500 " pdb=" O HOH A 646 " model vdw 2.122 2.170 ... (remaining 110787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'B' selection = (chain 'C' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.000 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.050 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:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13000 Z= 0.206 Angle : 0.482 6.696 17555 Z= 0.262 Chirality : 0.035 0.128 2020 Planarity : 0.005 0.096 2230 Dihedral : 16.924 89.866 4880 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.14 % Allowed : 23.56 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1575 helix: 0.68 (0.15), residues: 1000 sheet: 1.99 (0.42), residues: 145 loop : -0.91 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 196 HIS 0.003 0.001 HIS E 331 PHE 0.006 0.001 PHE B 352 TYR 0.008 0.001 TYR D 299 ARG 0.001 0.000 ARG C 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.421 Fit side-chains REVERT: C 203 LYS cc_start: 0.8819 (mttt) cc_final: 0.8614 (mttt) REVERT: C 270 VAL cc_start: 0.7502 (t) cc_final: 0.6930 (m) REVERT: E 170 GLN cc_start: 0.8549 (mt0) cc_final: 0.8324 (mt0) REVERT: E 368 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: E 390 ARG cc_start: 0.7275 (mmt180) cc_final: 0.7022 (mmt180) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 1.2076 time to fit residues: 262.4539 Evaluate side-chains 181 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 368 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 122 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 122 HIS ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN C 121 GLN C 122 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN C 298 ASN D 121 GLN D 122 HIS ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN D 298 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13000 Z= 0.260 Angle : 0.520 9.002 17555 Z= 0.271 Chirality : 0.039 0.129 2020 Planarity : 0.005 0.064 2230 Dihedral : 5.167 33.325 1740 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.99 % Allowed : 20.85 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1575 helix: 2.07 (0.16), residues: 1035 sheet: 2.01 (0.41), residues: 145 loop : -0.63 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 196 HIS 0.005 0.001 HIS B 331 PHE 0.020 0.002 PHE E 186 TYR 0.015 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 183 time to evaluate : 1.607 Fit side-chains REVERT: A 270 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.6963 (m) REVERT: B 138 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 270 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7074 (m) REVERT: B 337 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8222 (ttp-110) REVERT: C 124 MET cc_start: 0.9117 (tpt) cc_final: 0.8839 (tpt) REVERT: C 203 LYS cc_start: 0.8792 (mttt) cc_final: 0.8577 (mttt) REVERT: C 270 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.6957 (m) REVERT: D 270 VAL cc_start: 0.7513 (t) cc_final: 0.7082 (m) REVERT: E 270 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7024 (m) REVERT: E 337 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8246 (ttp-110) outliers start: 56 outliers final: 19 residues processed: 225 average time/residue: 1.2558 time to fit residues: 307.7943 Evaluate side-chains 198 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 327 ASN B 121 GLN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN E 122 HIS E 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13000 Z= 0.260 Angle : 0.518 9.059 17555 Z= 0.267 Chirality : 0.039 0.132 2020 Planarity : 0.004 0.052 2230 Dihedral : 4.054 31.389 1710 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.70 % Allowed : 20.43 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.22), residues: 1575 helix: 2.36 (0.16), residues: 1035 sheet: 1.74 (0.40), residues: 145 loop : -0.48 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.005 0.001 HIS B 331 PHE 0.019 0.002 PHE E 359 TYR 0.016 0.002 TYR D 299 ARG 0.004 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 180 time to evaluate : 1.450 Fit side-chains REVERT: A 270 VAL cc_start: 0.7383 (t) cc_final: 0.6947 (m) REVERT: B 138 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: B 270 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7058 (m) REVERT: B 337 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8213 (ttp-110) REVERT: C 203 LYS cc_start: 0.8784 (mttt) cc_final: 0.8560 (mttt) REVERT: C 270 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7022 (m) REVERT: C 387 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7467 (mt) REVERT: D 270 VAL cc_start: 0.7536 (t) cc_final: 0.7133 (m) REVERT: E 124 MET cc_start: 0.9201 (tpt) cc_final: 0.8855 (tpt) REVERT: E 270 VAL cc_start: 0.7462 (t) cc_final: 0.7052 (m) REVERT: E 337 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8242 (ttp-110) outliers start: 66 outliers final: 29 residues processed: 230 average time/residue: 1.0974 time to fit residues: 278.3352 Evaluate side-chains 210 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN E 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13000 Z= 0.232 Angle : 0.503 9.056 17555 Z= 0.258 Chirality : 0.038 0.132 2020 Planarity : 0.004 0.048 2230 Dihedral : 3.994 30.417 1710 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.34 % Allowed : 20.28 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.22), residues: 1575 helix: 2.46 (0.16), residues: 1035 sheet: 1.65 (0.40), residues: 145 loop : -0.48 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.005 0.001 HIS B 331 PHE 0.022 0.002 PHE E 186 TYR 0.015 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 176 time to evaluate : 1.384 Fit side-chains REVERT: A 138 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 270 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.6952 (m) REVERT: B 138 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 270 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7073 (m) REVERT: B 337 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (ttp-110) REVERT: C 124 MET cc_start: 0.9243 (tpt) cc_final: 0.8995 (tpt) REVERT: C 160 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: C 203 LYS cc_start: 0.8781 (mttt) cc_final: 0.8561 (mttt) REVERT: C 270 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7024 (m) REVERT: C 387 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (mt) REVERT: D 210 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7887 (mt) REVERT: D 270 VAL cc_start: 0.7546 (t) cc_final: 0.7157 (m) REVERT: D 363 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (mp) REVERT: E 337 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8325 (ttp-110) outliers start: 75 outliers final: 29 residues processed: 230 average time/residue: 1.1561 time to fit residues: 291.6919 Evaluate side-chains 212 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 298 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN D 131 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13000 Z= 0.232 Angle : 0.503 9.094 17555 Z= 0.259 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.045 2230 Dihedral : 3.989 30.175 1710 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.56 % Allowed : 21.28 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1575 helix: 2.51 (0.16), residues: 1035 sheet: 1.63 (0.41), residues: 145 loop : -0.43 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.005 0.001 HIS B 331 PHE 0.019 0.002 PHE E 359 TYR 0.015 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 1.584 Fit side-chains REVERT: A 138 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: A 270 VAL cc_start: 0.7313 (t) cc_final: 0.6901 (m) REVERT: B 138 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 270 VAL cc_start: 0.7495 (t) cc_final: 0.7079 (m) REVERT: B 337 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8258 (ttp-110) REVERT: C 124 MET cc_start: 0.9228 (tpt) cc_final: 0.8901 (tpt) REVERT: C 160 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: C 203 LYS cc_start: 0.8780 (mttt) cc_final: 0.8562 (mttt) REVERT: C 270 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7031 (m) REVERT: C 387 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7486 (mt) REVERT: D 210 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7886 (mt) REVERT: D 228 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5949 (mtt-85) REVERT: D 270 VAL cc_start: 0.7559 (t) cc_final: 0.7158 (m) REVERT: E 124 MET cc_start: 0.9200 (tpt) cc_final: 0.8718 (tpt) REVERT: E 270 VAL cc_start: 0.7500 (t) cc_final: 0.7084 (m) REVERT: E 337 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8324 (ttp-110) outliers start: 64 outliers final: 34 residues processed: 227 average time/residue: 1.1491 time to fit residues: 286.9394 Evaluate side-chains 218 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN D 131 ASN E 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13000 Z= 0.265 Angle : 0.524 9.385 17555 Z= 0.268 Chirality : 0.039 0.134 2020 Planarity : 0.004 0.043 2230 Dihedral : 4.058 31.247 1710 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.63 % Allowed : 21.21 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.22), residues: 1575 helix: 2.47 (0.16), residues: 1035 sheet: 1.61 (0.41), residues: 145 loop : -0.38 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.005 0.001 HIS B 331 PHE 0.024 0.002 PHE E 186 TYR 0.017 0.002 TYR D 299 ARG 0.004 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 179 time to evaluate : 1.576 Fit side-chains REVERT: A 138 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 270 VAL cc_start: 0.7376 (OUTLIER) cc_final: 0.6973 (m) REVERT: B 138 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 270 VAL cc_start: 0.7538 (t) cc_final: 0.7093 (m) REVERT: B 337 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8263 (ttp-110) REVERT: C 160 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6549 (mt-10) REVERT: C 203 LYS cc_start: 0.8782 (mttt) cc_final: 0.8567 (mttt) REVERT: C 270 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7051 (m) REVERT: C 387 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7510 (mt) REVERT: D 210 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7897 (mt) REVERT: D 270 VAL cc_start: 0.7554 (t) cc_final: 0.7178 (m) REVERT: E 124 MET cc_start: 0.9214 (tpt) cc_final: 0.8732 (tpt) REVERT: E 270 VAL cc_start: 0.7513 (t) cc_final: 0.7116 (m) REVERT: E 337 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8256 (ttp-110) outliers start: 65 outliers final: 33 residues processed: 227 average time/residue: 1.1539 time to fit residues: 288.2355 Evaluate side-chains 217 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN D 131 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13000 Z= 0.216 Angle : 0.496 9.107 17555 Z= 0.256 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.042 2230 Dihedral : 3.950 29.333 1710 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.13 % Allowed : 22.28 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.22), residues: 1575 helix: 2.57 (0.16), residues: 1035 sheet: 1.65 (0.41), residues: 145 loop : -0.37 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.004 0.001 HIS B 331 PHE 0.017 0.001 PHE A 186 TYR 0.014 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 1.560 Fit side-chains REVERT: A 138 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 270 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7002 (m) REVERT: B 138 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 270 VAL cc_start: 0.7519 (t) cc_final: 0.7071 (m) REVERT: B 337 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8209 (ttp-110) REVERT: C 160 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6551 (mt-10) REVERT: C 203 LYS cc_start: 0.8779 (mttt) cc_final: 0.8560 (mttt) REVERT: C 270 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7050 (m) REVERT: C 387 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7467 (mt) REVERT: D 210 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7882 (mt) REVERT: D 270 VAL cc_start: 0.7545 (t) cc_final: 0.7174 (m) REVERT: E 124 MET cc_start: 0.9203 (tpt) cc_final: 0.8707 (tpt) REVERT: E 138 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: E 160 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: E 270 VAL cc_start: 0.7510 (t) cc_final: 0.7109 (m) REVERT: E 337 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8218 (ttp-110) outliers start: 58 outliers final: 34 residues processed: 221 average time/residue: 1.1303 time to fit residues: 275.2246 Evaluate side-chains 219 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 298 ASN D 131 ASN E 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13000 Z= 0.308 Angle : 0.555 9.585 17555 Z= 0.284 Chirality : 0.040 0.134 2020 Planarity : 0.004 0.043 2230 Dihedral : 4.146 32.038 1710 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.56 % Allowed : 22.06 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.22), residues: 1575 helix: 2.35 (0.16), residues: 1040 sheet: 1.69 (0.42), residues: 145 loop : -0.54 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.007 0.001 HIS B 331 PHE 0.024 0.002 PHE E 186 TYR 0.018 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 180 time to evaluate : 1.394 Fit side-chains REVERT: A 138 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 268 LEU cc_start: 0.8415 (mt) cc_final: 0.8179 (mp) REVERT: A 270 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7022 (m) REVERT: B 138 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 270 VAL cc_start: 0.7566 (t) cc_final: 0.7066 (m) REVERT: B 337 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (ttp-110) REVERT: C 160 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6572 (mt-10) REVERT: C 203 LYS cc_start: 0.8783 (mttt) cc_final: 0.8570 (mttt) REVERT: C 270 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7087 (m) REVERT: C 387 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7516 (mt) REVERT: D 210 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (mt) REVERT: E 124 MET cc_start: 0.9230 (tpt) cc_final: 0.8745 (tpt) REVERT: E 138 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: E 270 VAL cc_start: 0.7539 (t) cc_final: 0.7152 (m) REVERT: E 337 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8281 (ttp-110) outliers start: 64 outliers final: 35 residues processed: 227 average time/residue: 1.1382 time to fit residues: 283.5588 Evaluate side-chains 219 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.005 0.033 13000 Z= 0.328 Angle : 0.576 9.650 17555 Z= 0.294 Chirality : 0.041 0.133 2020 Planarity : 0.004 0.045 2230 Dihedral : 4.198 32.075 1710 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.27 % Allowed : 22.78 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1575 helix: 2.25 (0.16), residues: 1040 sheet: 1.71 (0.42), residues: 145 loop : -0.53 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 196 HIS 0.007 0.001 HIS B 331 PHE 0.023 0.002 PHE B 359 TYR 0.019 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 177 time to evaluate : 1.578 Fit side-chains REVERT: A 138 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 210 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 268 LEU cc_start: 0.8411 (mt) cc_final: 0.8172 (mp) REVERT: A 270 VAL cc_start: 0.7448 (t) cc_final: 0.7015 (m) REVERT: B 138 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 270 VAL cc_start: 0.7573 (t) cc_final: 0.7063 (m) REVERT: B 337 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8293 (ttp-110) REVERT: C 160 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: C 270 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7056 (m) REVERT: C 387 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7511 (mt) REVERT: D 210 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (mt) REVERT: E 124 MET cc_start: 0.9217 (tpt) cc_final: 0.8749 (tpt) REVERT: E 138 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: E 270 VAL cc_start: 0.7578 (t) cc_final: 0.7184 (m) REVERT: E 337 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8266 (ttp-110) outliers start: 60 outliers final: 35 residues processed: 221 average time/residue: 1.1144 time to fit residues: 271.0618 Evaluate side-chains 219 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13000 Z= 0.169 Angle : 0.483 8.849 17555 Z= 0.250 Chirality : 0.037 0.132 2020 Planarity : 0.003 0.041 2230 Dihedral : 3.824 26.522 1710 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.56 % Allowed : 24.48 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.22), residues: 1575 helix: 2.64 (0.16), residues: 1040 sheet: 1.72 (0.41), residues: 145 loop : -0.57 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 196 HIS 0.002 0.001 HIS C 331 PHE 0.026 0.001 PHE E 186 TYR 0.010 0.001 TYR D 299 ARG 0.002 0.000 ARG D 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.610 Fit side-chains REVERT: A 138 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 270 VAL cc_start: 0.7385 (t) cc_final: 0.6960 (m) REVERT: A 338 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 138 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 270 VAL cc_start: 0.7459 (t) cc_final: 0.7058 (m) REVERT: B 337 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (ttp-110) REVERT: C 270 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7080 (m) REVERT: C 387 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7429 (mt) REVERT: D 210 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7877 (mt) REVERT: D 270 VAL cc_start: 0.7527 (t) cc_final: 0.7151 (m) REVERT: E 124 MET cc_start: 0.9170 (tpt) cc_final: 0.8655 (tpt) REVERT: E 270 VAL cc_start: 0.7486 (t) cc_final: 0.7140 (m) REVERT: E 337 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8284 (ttp-110) outliers start: 36 outliers final: 17 residues processed: 206 average time/residue: 1.1137 time to fit residues: 252.9088 Evaluate side-chains 195 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 298 ASN B 121 GLN B 327 ASN C 131 ASN C 298 ASN C 327 ASN D 131 ASN E 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.189001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122731 restraints weight = 11781.261| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.83 r_work: 0.2934 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 13000 Z= 0.528 Angle : 0.693 10.131 17555 Z= 0.351 Chirality : 0.047 0.152 2020 Planarity : 0.005 0.069 2230 Dihedral : 4.476 36.004 1710 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.27 % Allowed : 24.20 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.21), residues: 1575 helix: 2.14 (0.16), residues: 1000 sheet: 1.70 (0.43), residues: 145 loop : -0.80 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 196 HIS 0.012 0.002 HIS B 331 PHE 0.023 0.003 PHE E 186 TYR 0.021 0.003 TYR B 299 ARG 0.009 0.001 ARG B 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4810.49 seconds wall clock time: 84 minutes 36.10 seconds (5076.10 seconds total)