Starting phenix.real_space_refine on Fri Mar 15 23:15:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/03_2024/6wbi_21590_updated.pdb" } resolution = 4.39 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 8139 2.51 5 N 2392 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13018 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 373 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 2 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 373 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1860 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain breaks: 2 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 1000 Unresolved non-hydrogen dihedrals: 639 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 377 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1846 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 311} Chain breaks: 2 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 382 Chain: "E" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 382 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 382 Chain: "G" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1861 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 652 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 387 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'CBO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.91, per 1000 atoms: 0.68 Number of scatterers: 13018 At special positions: 0 Unit cell: (109.782, 105.678, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2452 8.00 N 2392 7.00 C 8139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.06 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.05 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: 6.55 Conformation dependent library (CDL) restraints added in 3.6 seconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 7 sheets defined 68.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 33 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 100 through 161 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix removed outlier: 3.974A pdb=" N ALA A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 208 through 235 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 270 through 295 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 327 through 336 removed outlier: 4.835A pdb=" N LEU A 335 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 336 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 33 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 100 through 161 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 208 through 236 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 295 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 327 through 336 removed outlier: 4.525A pdb=" N LEU B 335 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU B 336 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.506A pdb=" N SER B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 33 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 88 removed outlier: 3.546A pdb=" N VAL C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 109 through 161 Proline residue: C 123 - end of helix removed outlier: 4.915A pdb=" N ALA C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 208 through 236 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 270 through 295 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.542A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 5.025A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 33 through 53 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 100 through 130 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 133 through 161 Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.570A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 235 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 270 through 295 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.935A pdb=" N ILE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 343 through 357 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 33 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 100 through 129 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 161 removed outlier: 3.668A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 208 through 236 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 270 through 295 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.971A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 5.689A pdb=" N SER E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 357 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.739A pdb=" N SER F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 100 through 130 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 208 through 235 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 270 through 295 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 327 through 341 removed outlier: 5.213A pdb=" N SER F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 3 through 13 Processing helix chain 'G' and resid 33 through 53 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 100 through 129 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.700A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 236 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 270 through 295 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 305 through 311 removed outlier: 3.947A pdb=" N ILE G 311 " --> pdb=" O LYS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 4.816A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 Processing helix chain 'G' and resid 362 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= B, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= C, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= D, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= E, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= F, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= G, first strand: chain 'G' and resid 243 through 246 1093 hydrogen bonds defined for protein. 3201 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: 4.20 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 13191 1.57 - 1.93: 35 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 13227 Sorted by residual: bond pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 1.332 2.996 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CA ALA C 131 " pdb=" C ALA C 131 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.37e-02 5.33e+03 9.50e+00 bond pdb=" CA PHE A 244 " pdb=" CB PHE A 244 " ideal model delta sigma weight residual 1.535 1.502 0.034 2.09e-02 2.29e+03 2.60e+00 bond pdb=" CA PHE G 244 " pdb=" CB PHE G 244 " ideal model delta sigma weight residual 1.535 1.505 0.030 1.90e-02 2.77e+03 2.50e+00 bond pdb=" CA GLY C 360 " pdb=" C GLY C 360 " ideal model delta sigma weight residual 1.516 1.528 -0.012 8.20e-03 1.49e+04 2.08e+00 ... (remaining 13222 not shown) Histogram of bond angle deviations from ideal: 44.24 - 62.28: 1 62.28 - 80.32: 0 80.32 - 98.36: 0 98.36 - 116.41: 8562 116.41 - 134.45: 9866 Bond angle restraints: 18429 Sorted by residual: angle pdb=" O LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 122.59 44.24 78.35 1.33e+00 5.65e-01 3.47e+03 angle pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 121.54 134.45 -12.91 1.91e+00 2.74e-01 4.57e+01 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 112.80 108.01 4.79 1.15e+00 7.56e-01 1.73e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 122.79 -8.39 2.30e+00 1.89e-01 1.33e+01 angle pdb=" N SER F 239 " pdb=" CA SER F 239 " pdb=" C SER F 239 " ideal model delta sigma weight residual 113.72 108.71 5.01 1.52e+00 4.33e-01 1.09e+01 ... (remaining 18424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 7641 25.53 - 51.05: 89 51.05 - 76.58: 15 76.58 - 102.11: 6 102.11 - 127.63: 5 Dihedral angle restraints: 7756 sinusoidal: 1030 harmonic: 6726 Sorted by residual: dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta harmonic sigma weight residual 180.00 83.00 97.00 0 5.00e+00 4.00e-02 3.76e+02 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " pdb=" CB CYS B 265 " ideal model delta sinusoidal sigma weight residual 93.00 19.03 73.97 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 265 " pdb=" CB CYS C 265 " ideal model delta sinusoidal sigma weight residual 93.00 38.56 54.44 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2298 0.092 - 0.184: 70 0.184 - 0.276: 5 0.276 - 0.368: 1 0.368 - 0.460: 1 Chirality restraints: 2375 Sorted by residual: chirality pdb=" C9 CBO A 401 " pdb=" C10 CBO A 401 " pdb=" C11 CBO A 401 " pdb=" C8 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.68 -2.22 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C10 CBO A 401 " pdb=" C1 CBO A 401 " pdb=" C5 CBO A 401 " pdb=" C9 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.56 -2.84 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA CYS C 66 " pdb=" N CYS C 66 " pdb=" C CYS C 66 " pdb=" CB CYS C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2372 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 333 " -0.147 2.00e-02 2.50e+03 2.58e-01 6.64e+02 pdb=" C LEU B 333 " 0.395 2.00e-02 2.50e+03 pdb=" O LEU B 333 " -0.294 2.00e-02 2.50e+03 pdb=" N LEU B 335 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 74 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP C 74 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 74 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 74 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 123 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 124 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.021 5.00e-02 4.00e+02 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 259 2.67 - 3.23: 15439 3.23 - 3.79: 21874 3.79 - 4.34: 23890 4.34 - 4.90: 37013 Nonbonded interactions: 98475 Sorted by model distance: nonbonded pdb=" O TYR A 331 " pdb=" N LEU A 335 " model vdw 2.117 2.520 nonbonded pdb=" OG SER D 247 " pdb=" O ASP D 261 " model vdw 2.144 2.440 nonbonded pdb=" O TYR C 233 " pdb=" OG SER C 236 " model vdw 2.167 2.440 nonbonded pdb=" OG SER F 247 " pdb=" O ASP F 261 " model vdw 2.172 2.440 nonbonded pdb=" O SER C 65 " pdb=" N LYS C 266 " model vdw 2.190 2.520 ... (remaining 98470 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 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'B' and (resid 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'C' and (resid 2 through 30 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'D' and (resid 2 through 14 or resid 32 through 333 or resid 335 through \ 370)) selection = (chain 'E' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'F' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'G' and (resid 2 through 28 or resid 33 through 333 or resid 335 through \ 370)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.680 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 40.120 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.015 1.663 13227 Z= 0.452 Angle : 0.907 78.352 18429 Z= 0.588 Chirality : 0.043 0.460 2375 Planarity : 0.007 0.258 2522 Dihedral : 10.975 127.634 3296 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 1.00 % Allowed : 7.80 % Favored : 91.20 % 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: -0.82 (0.17), residues: 2238 helix: 0.15 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 74 HIS 0.007 0.001 HIS F 106 PHE 0.020 0.002 PHE D 235 TYR 0.020 0.001 TYR B 233 ARG 0.004 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 SER cc_start: 0.7972 (p) cc_final: 0.7748 (m) REVERT: E 38 VAL cc_start: 0.9335 (t) cc_final: 0.9056 (p) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.1902 time to fit residues: 34.8611 Evaluate side-chains 74 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS C 76 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 264 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13227 Z= 0.204 Angle : 0.557 7.955 18429 Z= 0.282 Chirality : 0.042 0.455 2375 Planarity : 0.004 0.042 2522 Dihedral : 7.992 131.496 2324 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 0.80 % Allowed : 4.60 % Favored : 94.60 % 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: 1.40 (0.18), residues: 2240 helix: 1.90 (0.13), residues: 1583 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.014 0.001 PHE G 129 TYR 0.016 0.001 TYR A 284 ARG 0.003 0.001 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 VAL cc_start: 0.9321 (t) cc_final: 0.9052 (p) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.1754 time to fit residues: 32.8905 Evaluate side-chains 78 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 50.0000 chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 203 optimal weight: 0.0270 chunk 220 optimal weight: 0.0970 chunk 181 optimal weight: 0.0070 chunk 202 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 overall best weight: 2.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 264 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13227 Z= 0.155 Angle : 0.529 8.235 18429 Z= 0.257 Chirality : 0.042 0.453 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.775 134.282 2324 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.20 % Allowed : 4.40 % Favored : 95.40 % 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: 2.48 (0.19), residues: 2240 helix: 2.72 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 104 HIS 0.006 0.001 HIS F 106 PHE 0.015 0.001 PHE G 12 TYR 0.026 0.001 TYR F 284 ARG 0.003 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 VAL cc_start: 0.9687 (t) cc_final: 0.9429 (p) REVERT: E 38 VAL cc_start: 0.9295 (t) cc_final: 0.9036 (p) REVERT: G 242 ASP cc_start: 0.7450 (p0) cc_final: 0.6772 (p0) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1690 time to fit residues: 32.4731 Evaluate side-chains 78 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 chunk 193 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13227 Z= 0.181 Angle : 0.533 7.929 18429 Z= 0.262 Chirality : 0.041 0.459 2375 Planarity : 0.004 0.046 2522 Dihedral : 7.739 131.893 2324 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 2.78 (0.19), residues: 2240 helix: 2.93 (0.13), residues: 1593 sheet: -4.42 (0.84), residues: 5 loop : -1.10 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 74 HIS 0.005 0.001 HIS F 106 PHE 0.018 0.001 PHE G 129 TYR 0.009 0.001 TYR G 284 ARG 0.003 0.001 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7643 (m-80) cc_final: 0.7335 (m-80) REVERT: E 38 VAL cc_start: 0.9337 (t) cc_final: 0.9109 (p) REVERT: G 242 ASP cc_start: 0.7992 (p0) cc_final: 0.7680 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1834 time to fit residues: 31.7860 Evaluate side-chains 77 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 184 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 0 optimal weight: 60.0000 chunk 110 optimal weight: 40.0000 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13227 Z= 0.215 Angle : 0.551 7.748 18429 Z= 0.277 Chirality : 0.042 0.463 2375 Planarity : 0.004 0.043 2522 Dihedral : 7.808 130.792 2324 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.20 % Allowed : 3.40 % Favored : 96.40 % 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: 2.89 (0.19), residues: 2240 helix: 2.96 (0.13), residues: 1593 sheet: -1.26 (1.69), residues: 14 loop : -0.90 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.001 PHE G 129 TYR 0.018 0.001 TYR F 284 ARG 0.004 0.001 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7721 (m-80) cc_final: 0.7498 (m-80) REVERT: E 38 VAL cc_start: 0.9382 (t) cc_final: 0.9159 (p) REVERT: G 242 ASP cc_start: 0.7419 (p0) cc_final: 0.6748 (p0) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1855 time to fit residues: 30.2920 Evaluate side-chains 70 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 127 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 0.0970 chunk 71 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13227 Z= 0.233 Angle : 0.568 10.330 18429 Z= 0.288 Chirality : 0.042 0.463 2375 Planarity : 0.004 0.044 2522 Dihedral : 7.848 130.817 2324 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.91 (0.19), residues: 2240 helix: 2.96 (0.13), residues: 1590 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.001 PHE E 235 TYR 0.029 0.001 TYR B 284 ARG 0.003 0.001 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: G 242 ASP cc_start: 0.7363 (p0) cc_final: 0.6774 (p0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1758 time to fit residues: 27.9877 Evaluate side-chains 70 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13227 Z= 0.336 Angle : 0.641 9.489 18429 Z= 0.341 Chirality : 0.043 0.476 2375 Planarity : 0.004 0.045 2522 Dihedral : 8.099 127.204 2324 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 2240 helix: 2.59 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 104 HIS 0.006 0.001 HIS F 106 PHE 0.019 0.002 PHE D 244 TYR 0.035 0.002 TYR B 284 ARG 0.003 0.001 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 240 LEU cc_start: 0.9292 (mt) cc_final: 0.9043 (pp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1593 time to fit residues: 25.1904 Evaluate side-chains 65 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 65 optimal weight: 0.1980 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13227 Z= 0.161 Angle : 0.551 9.822 18429 Z= 0.272 Chirality : 0.042 0.456 2375 Planarity : 0.004 0.046 2522 Dihedral : 7.847 135.605 2324 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 3.07 (0.19), residues: 2240 helix: 3.06 (0.13), residues: 1590 sheet: -3.36 (1.83), residues: 10 loop : -0.67 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.016 0.001 PHE G 129 TYR 0.029 0.001 TYR A 284 ARG 0.004 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8051 (pp20) cc_final: 0.7789 (pp20) REVERT: G 75 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8089 (mmt90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1853 time to fit residues: 31.1328 Evaluate side-chains 82 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 50.0000 chunk 206 optimal weight: 70.0000 chunk 188 optimal weight: 40.0000 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13227 Z= 0.194 Angle : 0.560 9.318 18429 Z= 0.279 Chirality : 0.042 0.470 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.801 132.365 2324 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 3.15 (0.19), residues: 2240 helix: 3.12 (0.13), residues: 1590 sheet: None (None), residues: 0 loop : -0.71 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 85 HIS 0.005 0.001 HIS F 106 PHE 0.018 0.001 PHE E 235 TYR 0.037 0.001 TYR B 284 ARG 0.005 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8118 (pp20) cc_final: 0.7828 (pp20) REVERT: A 282 VAL cc_start: 0.9696 (t) cc_final: 0.9458 (p) REVERT: G 75 ARG cc_start: 0.8398 (mmt90) cc_final: 0.8091 (mmt90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1747 time to fit residues: 27.8047 Evaluate side-chains 75 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 0.0370 chunk 223 optimal weight: 50.0000 chunk 205 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13227 Z= 0.160 Angle : 0.550 9.601 18429 Z= 0.269 Chirality : 0.042 0.461 2375 Planarity : 0.004 0.046 2522 Dihedral : 7.746 135.066 2324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 3.32 (0.19), residues: 2240 helix: 3.22 (0.13), residues: 1594 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.022 0.001 PHE G 129 TYR 0.035 0.001 TYR D 284 ARG 0.008 0.001 ARG E 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8094 (pp20) cc_final: 0.7816 (pp20) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2006 time to fit residues: 31.9096 Evaluate side-chains 74 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 50.0000 chunk 189 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 134 HIS ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.028683 restraints weight = 168048.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.029177 restraints weight = 128263.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029546 restraints weight = 104280.224| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13227 Z= 0.211 Angle : 0.565 9.054 18429 Z= 0.284 Chirality : 0.042 0.470 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.803 131.953 2324 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 3.23 (0.19), residues: 2240 helix: 3.16 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : -0.61 (0.27), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 127 HIS 0.005 0.001 HIS F 106 PHE 0.021 0.001 PHE G 129 TYR 0.033 0.001 TYR B 284 ARG 0.010 0.001 ARG E 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.60 seconds wall clock time: 34 minutes 32.94 seconds (2072.94 seconds total)