Starting phenix.real_space_refine on Sun Dec 10 02:05:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/12_2023/8tul_41624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/12_2023/8tul_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_41624/12_2023/8tul_41624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/12_2023/8tul_41624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/12_2023/8tul_41624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/12_2023/8tul_41624.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.23, per 1000 atoms: 0.55 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: 5.08 Conformation dependent library (CDL) restraints added in 2.3 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: 1.20 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: 3.95 Time building geometry restraints manager: 5.49 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: 1.480 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: 7.140 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 36.470 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.900 ------------------------------------------------------------------------------- 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 : 1.447 Fit side-chains outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 1.2307 time to fit residues: 268.2475 Evaluate side-chains 180 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 2.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 B 121 GLN B 122 HIS B 131 ASN B 298 ASN C 121 GLN C 122 HIS C 131 ASN 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 ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 298 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1201 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= 0.309 Angle : 0.547 9.190 17555 Z= 0.285 Chirality : 0.040 0.130 2020 Planarity : 0.005 0.071 2230 Dihedral : 3.725 12.848 1705 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.05 % Allowed : 19.64 % Favored : 75.30 % 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: 2.08 (0.22), residues: 1575 helix: 2.02 (0.16), residues: 1030 sheet: 1.98 (0.41), residues: 145 loop : -0.53 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.006 0.001 HIS B 331 PHE 0.020 0.002 PHE E 186 TYR 0.017 0.002 TYR D 299 ARG 0.004 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 249 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 178 time to evaluate : 1.715 Fit side-chains outliers start: 71 outliers final: 32 residues processed: 232 average time/residue: 1.3343 time to fit residues: 337.9211 Evaluate side-chains 205 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.2399 time to fit residues: 4.4649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 C 131 ASN D 131 ASN E 121 GLN E 122 HIS E 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13000 Z= 0.300 Angle : 0.542 9.386 17555 Z= 0.279 Chirality : 0.040 0.133 2020 Planarity : 0.005 0.064 2230 Dihedral : 3.786 13.441 1705 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.69 % Allowed : 19.15 % 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: 2.30 (0.22), residues: 1575 helix: 2.22 (0.16), residues: 1035 sheet: 1.74 (0.41), residues: 145 loop : -0.45 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.006 0.001 HIS B 331 PHE 0.017 0.002 PHE B 359 TYR 0.017 0.002 TYR C 299 ARG 0.005 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 249 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 169 time to evaluate : 1.525 Fit side-chains outliers start: 80 outliers final: 43 residues processed: 233 average time/residue: 1.1954 time to fit residues: 307.6397 Evaluate side-chains 213 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 37 residues processed: 6 average time/residue: 0.2464 time to fit residues: 4.2333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN D 131 ASN E 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1576 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= 0.237 Angle : 0.506 9.156 17555 Z= 0.261 Chirality : 0.039 0.132 2020 Planarity : 0.004 0.062 2230 Dihedral : 3.710 13.111 1705 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.98 % Allowed : 19.22 % Favored : 74.80 % 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: 2.47 (0.22), residues: 1575 helix: 2.40 (0.16), residues: 1035 sheet: 1.56 (0.41), residues: 145 loop : -0.43 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 196 HIS 0.005 0.001 HIS D 331 PHE 0.023 0.002 PHE E 186 TYR 0.016 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 258 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 174 time to evaluate : 1.653 Fit side-chains outliers start: 84 outliers final: 43 residues processed: 241 average time/residue: 1.1700 time to fit residues: 310.0616 Evaluate side-chains 214 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 0.2592 time to fit residues: 3.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 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 A 298 ASN A 327 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 327 ASN D 130 ASN D 131 ASN E 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13000 Z= 0.325 Angle : 0.562 9.674 17555 Z= 0.287 Chirality : 0.041 0.133 2020 Planarity : 0.005 0.061 2230 Dihedral : 3.863 13.949 1705 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.05 % Allowed : 20.21 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.22), residues: 1575 helix: 2.25 (0.16), residues: 1035 sheet: 1.52 (0.41), residues: 145 loop : -0.42 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.006 0.001 HIS B 331 PHE 0.019 0.002 PHE B 359 TYR 0.020 0.002 TYR D 299 ARG 0.005 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: 71 poor density : 172 time to evaluate : 1.509 Fit side-chains outliers start: 71 outliers final: 45 residues processed: 232 average time/residue: 1.1147 time to fit residues: 286.1885 Evaluate side-chains 216 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.2189 time to fit residues: 4.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 0.0030 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1719 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= 0.186 Angle : 0.478 9.066 17555 Z= 0.247 Chirality : 0.037 0.131 2020 Planarity : 0.004 0.059 2230 Dihedral : 3.635 13.146 1705 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.48 % Allowed : 21.14 % 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: 2.63 (0.22), residues: 1575 helix: 2.56 (0.16), residues: 1035 sheet: 1.52 (0.41), residues: 145 loop : -0.43 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 196 HIS 0.004 0.001 HIS D 331 PHE 0.025 0.001 PHE E 186 TYR 0.013 0.002 TYR D 299 ARG 0.002 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 235 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 1.625 Fit side-chains outliers start: 63 outliers final: 42 residues processed: 223 average time/residue: 1.1184 time to fit residues: 275.8311 Evaluate side-chains 207 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 38 residues processed: 4 average time/residue: 0.2763 time to fit residues: 3.6869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1717 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= 0.202 Angle : 0.492 9.101 17555 Z= 0.253 Chirality : 0.038 0.132 2020 Planarity : 0.004 0.059 2230 Dihedral : 3.612 13.307 1705 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.13 % Allowed : 22.06 % Favored : 73.81 % 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: 2.70 (0.22), residues: 1575 helix: 2.60 (0.16), residues: 1035 sheet: 1.56 (0.41), residues: 145 loop : -0.41 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 196 HIS 0.004 0.001 HIS B 331 PHE 0.019 0.001 PHE A 186 TYR 0.015 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 219 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 161 time to evaluate : 1.401 Fit side-chains outliers start: 58 outliers final: 40 residues processed: 208 average time/residue: 1.1648 time to fit residues: 266.8997 Evaluate side-chains 205 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.3049 time to fit residues: 3.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0010 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13000 Z= 0.245 Angle : 0.519 9.318 17555 Z= 0.266 Chirality : 0.039 0.132 2020 Planarity : 0.004 0.057 2230 Dihedral : 3.692 13.799 1705 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.06 % Allowed : 22.21 % Favored : 73.74 % 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: 1.61 (0.41), residues: 145 loop : -0.40 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 196 HIS 0.005 0.001 HIS B 331 PHE 0.022 0.002 PHE E 186 TYR 0.017 0.002 TYR D 299 ARG 0.004 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 217 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 1.536 Fit side-chains outliers start: 57 outliers final: 41 residues processed: 207 average time/residue: 1.2014 time to fit residues: 275.0637 Evaluate side-chains 197 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 4 average time/residue: 0.5729 time to fit residues: 4.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1698 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= 0.337 Angle : 0.573 9.616 17555 Z= 0.293 Chirality : 0.041 0.134 2020 Planarity : 0.004 0.056 2230 Dihedral : 3.859 13.770 1705 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.70 % Allowed : 22.63 % Favored : 73.67 % 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: 2.30 (0.22), residues: 1575 helix: 2.27 (0.16), residues: 1040 sheet: 1.64 (0.42), residues: 145 loop : -0.63 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 273 HIS 0.007 0.002 HIS B 331 PHE 0.023 0.002 PHE B 359 TYR 0.019 0.002 TYR D 299 ARG 0.006 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 219 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 167 time to evaluate : 1.498 Fit side-chains outliers start: 52 outliers final: 39 residues processed: 208 average time/residue: 1.1608 time to fit residues: 265.8552 Evaluate side-chains 203 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 37 residues processed: 2 average time/residue: 0.2804 time to fit residues: 2.8513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 102 optimal weight: 0.0970 chunk 154 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 194 GLN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1795 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= 0.204 Angle : 0.508 9.071 17555 Z= 0.262 Chirality : 0.038 0.131 2020 Planarity : 0.004 0.056 2230 Dihedral : 3.651 13.145 1705 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.99 % Allowed : 23.77 % Favored : 73.24 % 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: 2.56 (0.22), residues: 1575 helix: 2.52 (0.16), residues: 1040 sheet: 1.62 (0.41), residues: 145 loop : -0.65 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 196 HIS 0.004 0.001 HIS B 331 PHE 0.020 0.001 PHE A 186 TYR 0.014 0.002 TYR D 299 ARG 0.002 0.000 ARG B 332 ********************** 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 205 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 1.501 Fit side-chains outliers start: 42 outliers final: 38 residues processed: 204 average time/residue: 1.1329 time to fit residues: 255.4014 Evaluate side-chains 195 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 37 residues processed: 2 average time/residue: 0.2200 time to fit residues: 2.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 327 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.189733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121915 restraints weight = 11762.679| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.92 r_work: 0.2964 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1752 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= 0.326 Angle : 0.577 9.515 17555 Z= 0.295 Chirality : 0.041 0.134 2020 Planarity : 0.004 0.055 2230 Dihedral : 3.839 13.749 1705 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.27 % Allowed : 23.56 % Favored : 73.17 % 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: 2.33 (0.22), residues: 1575 helix: 2.30 (0.16), residues: 1040 sheet: 1.67 (0.42), residues: 145 loop : -0.64 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 196 HIS 0.007 0.001 HIS B 331 PHE 0.024 0.002 PHE E 186 TYR 0.019 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4782.89 seconds wall clock time: 85 minutes 44.54 seconds (5144.54 seconds total)