Starting phenix.real_space_refine on Tue Sep 24 19:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/09_2024/7y1r_33571.cif" } resolution = 4.01 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= 0.001 sd= 0.025 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 55 5.16 5 C 5432 2.51 5 N 1469 2.21 5 O 1609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8565 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2474 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 283} Chain breaks: 4 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2494 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 3 Chain: "E" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3332 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 23, 'TRANS': 404} Chain breaks: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.64 Number of scatterers: 8565 At special positions: 0 Unit cell: (98.115, 99.17, 132.93, 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 55 16.00 O 1609 8.00 N 1469 7.00 C 5432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 360 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B 401 " - " ASN B 53 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN B 107 " " NAG F 1 " - " ASN E 56 " " NAG G 1 " - " ASN E 137 " " NAG H 1 " - " ASN E 390 " " NAG I 1 " - " ASN E 214 " " NAG L 1 " - " ASN A 107 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 998.1 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 19 sheets defined 16.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.687A pdb=" N ASP A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.518A pdb=" N TYR A 92 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.908A pdb=" N GLY A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.394A pdb=" N CYS A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.507A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'B' and resid 5 through 28 removed outlier: 4.101A pdb=" N MET B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.714A pdb=" N ASP B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 4.183A pdb=" N LYS B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.264A pdb=" N ALA B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.751A pdb=" N GLN E 84 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 135 Processing helix chain 'E' and resid 326 through 332 removed outlier: 3.885A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.180A pdb=" N LYS A 77 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 341 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 346 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 339 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN B 352 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B 333 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.579A pdb=" N MET A 232 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG A 123 " --> pdb=" O MET A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 143 removed outlier: 4.557A pdb=" N SER A 154 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A 152 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 4.297A pdb=" N CYS A 265 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 292 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 272 removed outlier: 3.627A pdb=" N ILE A 271 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 288 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 338 removed outlier: 8.038A pdb=" N CYS A 327 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS A 358 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG A 356 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA A 331 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 354 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A 333 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 352 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.642A pdb=" N LEU B 231 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 128 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 167 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.038A pdb=" N PHE B 106 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 186 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 267 removed outlier: 3.906A pdb=" N CYS B 265 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 294 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 267 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 292 " --> pdb=" O ARG B 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 271 through 272 removed outlier: 3.835A pdb=" N ILE B 271 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 288 " --> pdb=" O ILE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 329 removed outlier: 3.905A pdb=" N VAL B 328 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 47 removed outlier: 6.494A pdb=" N LEU E 46 " --> pdb=" O HIS E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 94 removed outlier: 6.992A pdb=" N VAL E 144 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.862A pdb=" N LEU E 154 " --> pdb=" O GLU E 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.698A pdb=" N ARG E 190 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 237 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 202 removed outlier: 4.176A pdb=" N ILE E 202 " --> pdb=" O TRP E 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 349 through 350 removed outlier: 7.387A pdb=" N LEU E 349 " --> pdb=" O HIS E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 364 through 366 removed outlier: 3.519A pdb=" N SER E 392 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP E 414 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU E 391 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 450 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET E 415 " --> pdb=" O SER E 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.279A pdb=" N LEU E 472 " --> pdb=" O SER E 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 130 hydrogen bonds defined for protein. 351 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: 2.02 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2757 1.35 - 1.46: 2003 1.46 - 1.58: 3917 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 8754 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 8749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11381 1.50 - 2.99: 358 2.99 - 4.49: 80 4.49 - 5.99: 43 5.99 - 7.48: 12 Bond angle restraints: 11874 Sorted by residual: angle pdb=" C LYS A 280 " pdb=" N TRP A 281 " pdb=" CA TRP A 281 " ideal model delta sigma weight residual 121.58 115.05 6.53 1.95e+00 2.63e-01 1.12e+01 angle pdb=" CA ARG A 29 " pdb=" CB ARG A 29 " pdb=" CG ARG A 29 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.11e+00 angle pdb=" CA MET E 443 " pdb=" CB MET E 443 " pdb=" CG MET E 443 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.11e+00 angle pdb=" CA TRP A 281 " pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 113.60 118.60 -5.00 1.90e+00 2.77e-01 6.92e+00 angle pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.54e+00 ... (remaining 11869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 5162 22.59 - 45.17: 352 45.17 - 67.76: 26 67.76 - 90.34: 54 90.34 - 112.93: 23 Dihedral angle restraints: 5617 sinusoidal: 2562 harmonic: 3055 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS E 201 " pdb=" CB CYS E 201 " ideal model delta sinusoidal sigma weight residual 93.00 177.78 -84.78 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 264 " pdb=" SG CYS A 264 " pdb=" SG CYS A 327 " pdb=" CB CYS A 327 " ideal model delta sinusoidal sigma weight residual 93.00 170.99 -77.99 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS B 293 " pdb=" SG CYS B 293 " pdb=" SG CYS B 358 " pdb=" CB CYS B 358 " ideal model delta sinusoidal sigma weight residual 93.00 153.93 -60.93 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 5614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1161 0.054 - 0.109: 195 0.109 - 0.163: 20 0.163 - 0.217: 2 0.217 - 0.272: 6 Chirality restraints: 1384 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1381 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 159 " -0.064 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO B 160 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.020 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP A 281 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 279 " -0.016 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP A 279 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 279 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 279 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 279 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 279 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 279 " -0.002 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1126 2.76 - 3.30: 7937 3.30 - 3.83: 13107 3.83 - 4.37: 14297 4.37 - 4.90: 24519 Nonbonded interactions: 60986 Sorted by model distance: nonbonded pdb=" OG SER E 100 " pdb=" OE1 GLU E 101 " model vdw 2.227 3.040 nonbonded pdb=" O ALA B 76 " pdb=" OG1 THR B 234 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU B 125 " pdb=" OG SER B 168 " model vdw 2.273 3.040 nonbonded pdb=" O SER E 337 " pdb=" OG1 THR E 361 " model vdw 2.291 3.040 nonbonded pdb=" ND2 ASN A 155 " pdb=" OH TYR B 152 " model vdw 2.322 3.120 ... (remaining 60981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 196 or resid 225 through 240 or resid 255 throug \ h 361)) selection = (chain 'B' and (resid 4 through 60 or resid 73 through 180 or resid 188 through \ 196 or resid 225 through 240 or resid 255 through 361)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 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 0.076 8754 Z= 0.206 Angle : 0.704 7.482 11874 Z= 0.303 Chirality : 0.044 0.272 1384 Planarity : 0.005 0.099 1497 Dihedral : 17.910 112.926 3592 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.79 (0.24), residues: 1017 helix: 0.25 (0.46), residues: 130 sheet: -1.23 (0.49), residues: 125 loop : -2.57 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 281 HIS 0.006 0.001 HIS A 138 PHE 0.012 0.001 PHE A 257 TYR 0.023 0.001 TYR B 74 ARG 0.006 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7826 (tp40) cc_final: 0.7563 (tp-100) REVERT: A 228 PHE cc_start: 0.7472 (p90) cc_final: 0.7257 (p90) REVERT: B 18 GLU cc_start: 0.7836 (tp30) cc_final: 0.7597 (tp30) REVERT: B 314 TYR cc_start: 0.6555 (t80) cc_final: 0.6184 (t80) REVERT: B 333 GLU cc_start: 0.6760 (mp0) cc_final: 0.6530 (mp0) REVERT: E 414 ASP cc_start: 0.5281 (p0) cc_final: 0.4900 (p0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2518 time to fit residues: 56.0738 Evaluate side-chains 157 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.0060 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8754 Z= 0.192 Angle : 0.679 8.976 11874 Z= 0.305 Chirality : 0.045 0.305 1384 Planarity : 0.005 0.080 1497 Dihedral : 11.756 94.643 1549 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.80 (0.24), residues: 1017 helix: 0.17 (0.45), residues: 128 sheet: -1.65 (0.44), residues: 148 loop : -2.48 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.007 0.001 HIS B 138 PHE 0.012 0.001 PHE A 106 TYR 0.011 0.001 TYR B 52 ARG 0.005 0.001 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7935 (tp40) cc_final: 0.7610 (tp-100) REVERT: A 77 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7860 (mtpp) REVERT: A 84 MET cc_start: 0.4923 (tpt) cc_final: 0.4491 (tpt) REVERT: A 111 LEU cc_start: 0.6758 (mm) cc_final: 0.6558 (mt) REVERT: A 151 ARG cc_start: 0.6967 (ptp90) cc_final: 0.6612 (ptp90) REVERT: A 339 TYR cc_start: 0.6826 (p90) cc_final: 0.6605 (p90) REVERT: A 346 LYS cc_start: 0.8345 (pttm) cc_final: 0.7963 (pttm) REVERT: B 15 LYS cc_start: 0.8270 (tppt) cc_final: 0.7642 (tppt) REVERT: B 18 GLU cc_start: 0.7837 (tp30) cc_final: 0.7570 (tp30) REVERT: B 74 TYR cc_start: 0.6621 (t80) cc_final: 0.6356 (t80) REVERT: B 302 SER cc_start: 0.6848 (t) cc_final: 0.6402 (t) REVERT: B 314 TYR cc_start: 0.6947 (t80) cc_final: 0.6720 (t80) REVERT: B 353 MET cc_start: 0.7949 (mmp) cc_final: 0.7541 (mmp) REVERT: E 90 ARG cc_start: 0.6741 (tpp-160) cc_final: 0.6358 (tpp-160) REVERT: E 414 ASP cc_start: 0.5882 (p0) cc_final: 0.5566 (p0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2204 time to fit residues: 51.1908 Evaluate side-chains 159 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN E 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8754 Z= 0.146 Angle : 0.628 9.477 11874 Z= 0.278 Chirality : 0.043 0.239 1384 Planarity : 0.004 0.062 1497 Dihedral : 9.798 90.405 1549 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.80 (0.24), residues: 1017 helix: 0.25 (0.46), residues: 127 sheet: -1.75 (0.43), residues: 156 loop : -2.46 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 301 HIS 0.003 0.001 HIS A 193 PHE 0.008 0.001 PHE B 105 TYR 0.019 0.001 TYR A 52 ARG 0.005 0.000 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7828 (t) cc_final: 0.7554 (p) REVERT: A 84 MET cc_start: 0.4905 (tpt) cc_final: 0.4526 (tpt) REVERT: A 151 ARG cc_start: 0.7055 (ptp90) cc_final: 0.6580 (ptp90) REVERT: A 333 GLU cc_start: 0.6236 (pt0) cc_final: 0.6008 (pt0) REVERT: A 339 TYR cc_start: 0.6792 (p90) cc_final: 0.6543 (p90) REVERT: A 346 LYS cc_start: 0.8346 (pttm) cc_final: 0.8008 (pttp) REVERT: B 18 GLU cc_start: 0.7830 (tp30) cc_final: 0.7542 (tp30) REVERT: B 74 TYR cc_start: 0.6778 (t80) cc_final: 0.6510 (t80) REVERT: B 301 TRP cc_start: 0.7212 (m100) cc_final: 0.6704 (m100) REVERT: B 314 TYR cc_start: 0.6891 (t80) cc_final: 0.6684 (t80) REVERT: B 333 GLU cc_start: 0.7047 (mp0) cc_final: 0.6764 (mp0) REVERT: E 153 ARG cc_start: 0.7158 (mtp-110) cc_final: 0.6703 (mtp85) REVERT: E 319 GLN cc_start: 0.7939 (mp10) cc_final: 0.7634 (mp10) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2353 time to fit residues: 53.7320 Evaluate side-chains 158 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8754 Z= 0.189 Angle : 0.664 9.854 11874 Z= 0.300 Chirality : 0.043 0.282 1384 Planarity : 0.004 0.054 1497 Dihedral : 8.335 84.945 1549 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.59 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.24), residues: 1017 helix: 0.25 (0.45), residues: 133 sheet: -1.57 (0.43), residues: 160 loop : -2.46 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 279 HIS 0.007 0.001 HIS B 138 PHE 0.011 0.001 PHE E 314 TYR 0.013 0.001 TYR A 52 ARG 0.004 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7989 (t) cc_final: 0.7776 (p) REVERT: A 84 MET cc_start: 0.4760 (tpt) cc_final: 0.4380 (tpt) REVERT: A 151 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7442 (ptp90) REVERT: A 152 TYR cc_start: 0.6713 (t80) cc_final: 0.6286 (t80) REVERT: A 171 VAL cc_start: 0.7873 (m) cc_final: 0.7207 (t) REVERT: A 269 LEU cc_start: 0.7729 (tt) cc_final: 0.7487 (tt) REVERT: A 338 VAL cc_start: 0.7578 (t) cc_final: 0.7208 (p) REVERT: A 346 LYS cc_start: 0.8426 (pttm) cc_final: 0.8003 (pttp) REVERT: A 347 VAL cc_start: 0.8853 (p) cc_final: 0.8529 (m) REVERT: B 18 GLU cc_start: 0.7859 (tp30) cc_final: 0.7585 (tp30) REVERT: B 74 TYR cc_start: 0.6849 (t80) cc_final: 0.6529 (t80) REVERT: B 297 CYS cc_start: 0.6709 (m) cc_final: 0.6397 (m) REVERT: B 301 TRP cc_start: 0.7360 (m100) cc_final: 0.7070 (m100) REVERT: E 90 ARG cc_start: 0.6857 (tpp-160) cc_final: 0.6601 (tpp-160) REVERT: E 315 LEU cc_start: 0.8132 (tp) cc_final: 0.7169 (tt) REVERT: E 343 GLN cc_start: 0.7689 (pt0) cc_final: 0.7069 (pt0) REVERT: E 414 ASP cc_start: 0.6445 (p0) cc_final: 0.6233 (p0) REVERT: E 415 MET cc_start: 0.5962 (pmm) cc_final: 0.5746 (pmm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2080 time to fit residues: 50.3664 Evaluate side-chains 166 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 40 optimal weight: 0.0970 chunk 84 optimal weight: 0.2980 chunk 68 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 overall best weight: 0.1232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 143 GLN E 338 HIS E 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8754 Z= 0.138 Angle : 0.626 9.599 11874 Z= 0.277 Chirality : 0.041 0.232 1384 Planarity : 0.004 0.044 1497 Dihedral : 7.662 81.685 1549 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.65 (0.24), residues: 1017 helix: 0.36 (0.46), residues: 134 sheet: -1.54 (0.43), residues: 160 loop : -2.41 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.009 0.001 HIS A 283 PHE 0.011 0.001 PHE E 389 TYR 0.011 0.001 TYR A 288 ARG 0.006 0.000 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7911 (t) cc_final: 0.7692 (p) REVERT: A 81 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8041 (ptt90) REVERT: A 84 MET cc_start: 0.4807 (tpt) cc_final: 0.4415 (tpt) REVERT: A 151 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7391 (ptp90) REVERT: A 152 TYR cc_start: 0.6585 (t80) cc_final: 0.6266 (t80) REVERT: A 171 VAL cc_start: 0.7838 (m) cc_final: 0.7164 (t) REVERT: A 269 LEU cc_start: 0.7601 (tt) cc_final: 0.7186 (tt) REVERT: A 333 GLU cc_start: 0.6637 (pt0) cc_final: 0.6430 (pt0) REVERT: A 338 VAL cc_start: 0.7538 (t) cc_final: 0.7091 (p) REVERT: A 346 LYS cc_start: 0.8348 (pttm) cc_final: 0.8046 (pttp) REVERT: A 347 VAL cc_start: 0.8774 (p) cc_final: 0.8457 (m) REVERT: B 18 GLU cc_start: 0.7814 (tp30) cc_final: 0.7594 (tp30) REVERT: B 299 TYR cc_start: 0.6976 (t80) cc_final: 0.6668 (t80) REVERT: B 301 TRP cc_start: 0.7247 (m100) cc_final: 0.6970 (m100) REVERT: E 90 ARG cc_start: 0.6847 (tpp-160) cc_final: 0.6528 (tpp-160) REVERT: E 315 LEU cc_start: 0.8341 (tp) cc_final: 0.7993 (tt) REVERT: E 319 GLN cc_start: 0.7967 (mp10) cc_final: 0.7368 (mp10) REVERT: E 325 LEU cc_start: 0.6828 (tt) cc_final: 0.6185 (mm) REVERT: E 414 ASP cc_start: 0.6338 (p0) cc_final: 0.6024 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2306 time to fit residues: 55.0429 Evaluate side-chains 165 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8754 Z= 0.217 Angle : 0.714 9.840 11874 Z= 0.325 Chirality : 0.044 0.275 1384 Planarity : 0.005 0.058 1497 Dihedral : 7.642 79.208 1549 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.08 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.76 (0.24), residues: 1017 helix: 0.31 (0.46), residues: 134 sheet: -1.39 (0.44), residues: 155 loop : -2.56 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.009 0.001 HIS B 100 PHE 0.016 0.001 PHE E 389 TYR 0.018 0.002 TYR B 270 ARG 0.006 0.000 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8107 (ptt90) REVERT: A 84 MET cc_start: 0.5093 (tpt) cc_final: 0.4567 (tpt) REVERT: A 151 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7466 (ptp90) REVERT: A 152 TYR cc_start: 0.7019 (t80) cc_final: 0.6602 (t80) REVERT: A 171 VAL cc_start: 0.7793 (m) cc_final: 0.7146 (t) REVERT: A 232 MET cc_start: 0.6990 (mtm) cc_final: 0.6702 (mtm) REVERT: A 333 GLU cc_start: 0.7193 (pt0) cc_final: 0.6955 (pt0) REVERT: A 338 VAL cc_start: 0.7875 (t) cc_final: 0.7518 (p) REVERT: B 165 GLU cc_start: 0.7716 (pp20) cc_final: 0.7503 (pp20) REVERT: B 301 TRP cc_start: 0.7455 (m100) cc_final: 0.7242 (m100) REVERT: B 349 GLN cc_start: 0.7307 (tt0) cc_final: 0.7029 (tt0) REVERT: B 357 SER cc_start: 0.6799 (p) cc_final: 0.6578 (p) REVERT: E 90 ARG cc_start: 0.6875 (tpp-160) cc_final: 0.6508 (tpp-160) REVERT: E 315 LEU cc_start: 0.8288 (tp) cc_final: 0.7907 (tp) REVERT: E 319 GLN cc_start: 0.7890 (mp10) cc_final: 0.7573 (mp10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2099 time to fit residues: 51.8367 Evaluate side-chains 170 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8754 Z= 0.186 Angle : 0.682 9.885 11874 Z= 0.309 Chirality : 0.043 0.258 1384 Planarity : 0.005 0.058 1497 Dihedral : 7.358 75.222 1549 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.59 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.77 (0.24), residues: 1017 helix: 0.41 (0.46), residues: 128 sheet: -1.56 (0.42), residues: 161 loop : -2.52 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 279 HIS 0.010 0.001 HIS B 100 PHE 0.015 0.001 PHE E 389 TYR 0.024 0.001 TYR B 74 ARG 0.008 0.000 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8109 (ptt90) REVERT: A 84 MET cc_start: 0.5141 (tpt) cc_final: 0.4711 (tpt) REVERT: A 151 ARG cc_start: 0.7871 (ptp90) cc_final: 0.7488 (ptp90) REVERT: A 152 TYR cc_start: 0.6973 (t80) cc_final: 0.6619 (t80) REVERT: A 171 VAL cc_start: 0.7840 (m) cc_final: 0.7210 (t) REVERT: A 269 LEU cc_start: 0.8101 (tt) cc_final: 0.7807 (tt) REVERT: A 333 GLU cc_start: 0.7335 (pt0) cc_final: 0.7080 (pt0) REVERT: A 338 VAL cc_start: 0.7787 (t) cc_final: 0.7455 (p) REVERT: A 346 LYS cc_start: 0.8424 (pttp) cc_final: 0.8206 (pttp) REVERT: B 224 MET cc_start: 0.4260 (mpp) cc_final: 0.3960 (mpp) REVERT: E 90 ARG cc_start: 0.6939 (tpp-160) cc_final: 0.6517 (tpp-160) REVERT: E 146 LEU cc_start: 0.8379 (mt) cc_final: 0.8168 (mt) REVERT: E 315 LEU cc_start: 0.8252 (tp) cc_final: 0.7935 (tp) REVERT: E 319 GLN cc_start: 0.7933 (mp10) cc_final: 0.7224 (mp10) REVERT: E 339 LEU cc_start: 0.8337 (tp) cc_final: 0.8125 (tt) REVERT: E 389 PHE cc_start: 0.7309 (t80) cc_final: 0.6819 (t80) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2368 time to fit residues: 57.4237 Evaluate side-chains 170 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 48 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8754 Z= 0.150 Angle : 0.664 10.181 11874 Z= 0.298 Chirality : 0.042 0.250 1384 Planarity : 0.004 0.053 1497 Dihedral : 6.957 71.681 1549 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.24), residues: 1017 helix: 0.48 (0.46), residues: 129 sheet: -1.48 (0.43), residues: 156 loop : -2.48 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 301 HIS 0.009 0.001 HIS B 100 PHE 0.014 0.001 PHE A 228 TYR 0.025 0.001 TYR A 52 ARG 0.006 0.000 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8079 (ptt90) REVERT: A 84 MET cc_start: 0.5306 (tpt) cc_final: 0.4863 (tpt) REVERT: A 151 ARG cc_start: 0.7893 (ptp90) cc_final: 0.7507 (ptp90) REVERT: A 152 TYR cc_start: 0.6981 (t80) cc_final: 0.6610 (t80) REVERT: A 171 VAL cc_start: 0.7846 (m) cc_final: 0.7156 (t) REVERT: A 333 GLU cc_start: 0.7360 (pt0) cc_final: 0.7132 (pt0) REVERT: A 338 VAL cc_start: 0.7744 (t) cc_final: 0.7398 (p) REVERT: B 74 TYR cc_start: 0.7300 (t80) cc_final: 0.6907 (t80) REVERT: B 224 MET cc_start: 0.4252 (mpp) cc_final: 0.3878 (mpp) REVERT: B 292 PHE cc_start: 0.7020 (p90) cc_final: 0.6815 (p90) REVERT: B 357 SER cc_start: 0.6853 (p) cc_final: 0.6625 (p) REVERT: E 90 ARG cc_start: 0.6919 (tpp-160) cc_final: 0.6495 (tpp-160) REVERT: E 212 VAL cc_start: 0.8649 (p) cc_final: 0.8411 (t) REVERT: E 315 LEU cc_start: 0.8205 (tp) cc_final: 0.7831 (tp) REVERT: E 389 PHE cc_start: 0.7261 (t80) cc_final: 0.6859 (t80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2448 time to fit residues: 59.5596 Evaluate side-chains 168 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 342 HIS E 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8754 Z= 0.162 Angle : 0.678 10.160 11874 Z= 0.303 Chirality : 0.042 0.255 1384 Planarity : 0.004 0.052 1497 Dihedral : 6.820 68.612 1549 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.71 (0.24), residues: 1017 helix: 0.45 (0.46), residues: 128 sheet: -1.73 (0.40), residues: 170 loop : -2.42 (0.20), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 301 HIS 0.009 0.001 HIS B 100 PHE 0.011 0.001 PHE E 389 TYR 0.012 0.001 TYR A 52 ARG 0.005 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8091 (ptt90) REVERT: A 151 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7539 (ptp90) REVERT: A 152 TYR cc_start: 0.7000 (t80) cc_final: 0.6667 (t80) REVERT: A 171 VAL cc_start: 0.7899 (m) cc_final: 0.7180 (t) REVERT: A 333 GLU cc_start: 0.7413 (pt0) cc_final: 0.7157 (pt0) REVERT: A 338 VAL cc_start: 0.7780 (t) cc_final: 0.7437 (p) REVERT: B 224 MET cc_start: 0.4263 (mpp) cc_final: 0.3819 (mpp) REVERT: E 90 ARG cc_start: 0.6942 (tpp-160) cc_final: 0.6510 (tpp-160) REVERT: E 212 VAL cc_start: 0.8670 (p) cc_final: 0.8446 (t) REVERT: E 315 LEU cc_start: 0.7924 (tp) cc_final: 0.7628 (tt) REVERT: E 317 MET cc_start: 0.6683 (mtm) cc_final: 0.6475 (mtp) REVERT: E 319 GLN cc_start: 0.8190 (mp10) cc_final: 0.7494 (mp10) REVERT: E 389 PHE cc_start: 0.7250 (t80) cc_final: 0.6777 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2440 time to fit residues: 58.3116 Evaluate side-chains 171 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 74 optimal weight: 0.0170 chunk 11 optimal weight: 4.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 342 HIS E 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8754 Z= 0.160 Angle : 0.687 10.157 11874 Z= 0.308 Chirality : 0.042 0.251 1384 Planarity : 0.004 0.051 1497 Dihedral : 6.669 65.608 1549 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.68 (0.24), residues: 1017 helix: 0.48 (0.46), residues: 128 sheet: -1.76 (0.41), residues: 165 loop : -2.39 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 301 HIS 0.009 0.001 HIS B 100 PHE 0.010 0.001 PHE E 389 TYR 0.027 0.001 TYR B 145 ARG 0.005 0.000 ARG E 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8091 (ptt90) REVERT: A 84 MET cc_start: 0.5233 (tpt) cc_final: 0.4812 (tpt) REVERT: A 151 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7557 (ptp90) REVERT: A 171 VAL cc_start: 0.7914 (m) cc_final: 0.7260 (t) REVERT: A 333 GLU cc_start: 0.7438 (pt0) cc_final: 0.7148 (pt0) REVERT: A 338 VAL cc_start: 0.7773 (t) cc_final: 0.7423 (p) REVERT: B 349 GLN cc_start: 0.7266 (tt0) cc_final: 0.6984 (tt0) REVERT: E 90 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6513 (tpp-160) REVERT: E 146 LEU cc_start: 0.8302 (mt) cc_final: 0.8096 (mt) REVERT: E 212 VAL cc_start: 0.8671 (p) cc_final: 0.8447 (t) REVERT: E 315 LEU cc_start: 0.7907 (tp) cc_final: 0.7600 (tp) REVERT: E 317 MET cc_start: 0.6685 (mtm) cc_final: 0.6467 (mtm) REVERT: E 319 GLN cc_start: 0.8133 (mp10) cc_final: 0.7486 (mp10) REVERT: E 389 PHE cc_start: 0.7294 (t80) cc_final: 0.6770 (t80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1776 time to fit residues: 41.8346 Evaluate side-chains 170 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 54 optimal weight: 0.0060 overall best weight: 0.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 342 HIS E 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.188326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167624 restraints weight = 15078.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171782 restraints weight = 9159.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.174635 restraints weight = 6350.903| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8754 Z= 0.150 Angle : 0.664 9.623 11874 Z= 0.298 Chirality : 0.041 0.234 1384 Planarity : 0.004 0.050 1497 Dihedral : 6.277 59.442 1549 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.61 (0.24), residues: 1017 helix: 0.62 (0.46), residues: 128 sheet: -1.92 (0.42), residues: 161 loop : -2.30 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 301 HIS 0.009 0.001 HIS B 100 PHE 0.008 0.001 PHE E 389 TYR 0.017 0.001 TYR B 270 ARG 0.004 0.000 ARG E 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.00 seconds wall clock time: 41 minutes 38.65 seconds (2498.65 seconds total)