Starting phenix.real_space_refine on Mon May 12 03:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_33571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_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/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_33571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_33571.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_33571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1r_33571/05_2025/7y1r_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-5687/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: 5.28, per 1000 atoms: 0.62 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 1.97 Time building geometry restraints manager: 2.78 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: 1.040 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.600 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- 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 8787 Z= 0.158 Angle : 0.712 7.482 11960 Z= 0.305 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 1.84553 ( 24) link_BETA1-4 : bond 0.00397 ( 11) link_BETA1-4 : angle 1.37530 ( 33) hydrogen bonds : bond 0.22318 ( 130) hydrogen bonds : angle 7.91424 ( 351) SS BOND : bond 0.00129 ( 13) SS BOND : angle 0.77790 ( 26) link_BETA1-3 : bond 0.01056 ( 1) link_BETA1-3 : angle 1.71039 ( 3) covalent geometry : bond 0.00330 ( 8754) covalent geometry : angle 0.70418 (11874) *********************** 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 to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.871 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: 0.2287 time to fit residues: 51.0264 Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 343 GLN E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.197739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176755 restraints weight = 15360.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180846 restraints weight = 9408.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.183751 restraints weight = 6564.785| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8787 Z= 0.149 Angle : 0.740 9.237 11960 Z= 0.328 Chirality : 0.047 0.324 1384 Planarity : 0.005 0.080 1497 Dihedral : 10.890 91.869 1549 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % 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: -2.85 (0.24), residues: 1017 helix: 0.09 (0.45), residues: 128 sheet: -1.70 (0.44), residues: 148 loop : -2.50 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.009 0.001 HIS B 138 PHE 0.013 0.001 PHE A 106 TYR 0.019 0.002 TYR A 152 ARG 0.005 0.001 ARG A 176 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 8) link_NAG-ASN : angle 2.19301 ( 24) link_BETA1-4 : bond 0.00650 ( 11) link_BETA1-4 : angle 3.26311 ( 33) hydrogen bonds : bond 0.03107 ( 130) hydrogen bonds : angle 5.06990 ( 351) SS BOND : bond 0.00285 ( 13) SS BOND : angle 1.03220 ( 26) link_BETA1-3 : bond 0.00382 ( 1) link_BETA1-3 : angle 3.89713 ( 3) covalent geometry : bond 0.00329 ( 8754) covalent geometry : angle 0.71171 (11874) *********************** 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 174 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7905 (tp40) cc_final: 0.7556 (tp-100) REVERT: A 77 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7800 (mtpp) REVERT: A 84 MET cc_start: 0.4978 (tpt) cc_final: 0.4562 (tpt) REVERT: A 111 LEU cc_start: 0.6767 (mm) cc_final: 0.6521 (mt) REVERT: A 151 ARG cc_start: 0.7031 (ptp90) cc_final: 0.6669 (ptp90) REVERT: A 279 TRP cc_start: 0.7880 (p90) cc_final: 0.7669 (p90) REVERT: A 346 LYS cc_start: 0.8362 (pttm) cc_final: 0.7927 (pttm) REVERT: B 15 LYS cc_start: 0.8379 (tppt) cc_final: 0.7781 (tppt) REVERT: B 74 TYR cc_start: 0.6669 (t80) cc_final: 0.6409 (t80) REVERT: B 353 MET cc_start: 0.7962 (mmp) cc_final: 0.7589 (mmp) REVERT: E 90 ARG cc_start: 0.6758 (tpp-160) cc_final: 0.6405 (tpp-160) REVERT: E 319 GLN cc_start: 0.7906 (mp10) cc_final: 0.7644 (mp10) REVERT: E 414 ASP cc_start: 0.6207 (p0) cc_final: 0.5920 (p0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2244 time to fit residues: 52.5776 Evaluate side-chains 158 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 177 GLN B 349 GLN E 71 HIS E 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158245 restraints weight = 14929.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162130 restraints weight = 9241.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.164804 restraints weight = 6494.819| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 8787 Z= 0.326 Angle : 1.022 12.037 11960 Z= 0.485 Chirality : 0.055 0.335 1384 Planarity : 0.007 0.076 1497 Dihedral : 11.523 89.951 1549 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.13 % Favored : 89.77 % Rotamer: Outliers : 0.43 % Allowed : 8.96 % Favored : 90.60 % 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: -3.49 (0.23), residues: 1017 helix: -1.30 (0.41), residues: 137 sheet: -1.68 (0.40), residues: 162 loop : -2.90 (0.19), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP A 281 HIS 0.013 0.003 HIS B 138 PHE 0.025 0.003 PHE E 314 TYR 0.034 0.003 TYR A 52 ARG 0.009 0.001 ARG E 501 Details of bonding type rmsd link_NAG-ASN : bond 0.01630 ( 8) link_NAG-ASN : angle 3.83134 ( 24) link_BETA1-4 : bond 0.00518 ( 11) link_BETA1-4 : angle 2.34453 ( 33) hydrogen bonds : bond 0.06111 ( 130) hydrogen bonds : angle 5.63043 ( 351) SS BOND : bond 0.00517 ( 13) SS BOND : angle 1.57599 ( 26) link_BETA1-3 : bond 0.00292 ( 1) link_BETA1-3 : angle 3.98468 ( 3) covalent geometry : bond 0.00714 ( 8754) covalent geometry : angle 0.99876 (11874) *********************** 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 196 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8025 (tp40) cc_final: 0.7804 (tp-100) REVERT: A 151 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7495 (ptp90) REVERT: A 152 TYR cc_start: 0.7266 (t80) cc_final: 0.6869 (t80) REVERT: A 171 VAL cc_start: 0.8142 (m) cc_final: 0.7637 (t) REVERT: A 333 GLU cc_start: 0.7690 (pt0) cc_final: 0.7254 (pt0) REVERT: A 339 TYR cc_start: 0.7605 (p90) cc_final: 0.7347 (p90) REVERT: A 346 LYS cc_start: 0.8546 (pttm) cc_final: 0.8310 (pttp) REVERT: B 27 LYS cc_start: 0.7871 (tptt) cc_final: 0.7529 (mmmt) REVERT: B 283 HIS cc_start: 0.7505 (m90) cc_final: 0.7285 (m-70) REVERT: B 291 ASN cc_start: 0.8096 (m110) cc_final: 0.7873 (m110) REVERT: B 348 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6837 (mt-10) REVERT: B 352 ASN cc_start: 0.8264 (m-40) cc_final: 0.7899 (m-40) REVERT: B 353 MET cc_start: 0.8004 (mmp) cc_final: 0.7363 (mmm) REVERT: B 355 VAL cc_start: 0.8233 (p) cc_final: 0.8000 (m) REVERT: E 43 MET cc_start: 0.6218 (mmp) cc_final: 0.6013 (mmp) REVERT: E 215 VAL cc_start: 0.8747 (t) cc_final: 0.8304 (p) REVERT: E 233 GLU cc_start: 0.6680 (pp20) cc_final: 0.6475 (pp20) REVERT: E 257 ARG cc_start: 0.7308 (ptm160) cc_final: 0.7012 (ptm-80) REVERT: E 315 LEU cc_start: 0.8079 (tp) cc_final: 0.7570 (tp) REVERT: E 317 MET cc_start: 0.7311 (mtp) cc_final: 0.6381 (mtp) REVERT: E 318 SER cc_start: 0.7789 (p) cc_final: 0.6981 (p) REVERT: E 443 MET cc_start: 0.6508 (ppp) cc_final: 0.6055 (ptt) outliers start: 4 outliers final: 2 residues processed: 194 average time/residue: 0.2359 time to fit residues: 59.7760 Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159314 restraints weight = 14941.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163281 restraints weight = 9185.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166035 restraints weight = 6468.603| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8787 Z= 0.150 Angle : 0.775 12.512 11960 Z= 0.349 Chirality : 0.046 0.265 1384 Planarity : 0.005 0.071 1497 Dihedral : 9.838 85.668 1549 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -3.16 (0.24), residues: 1017 helix: -0.49 (0.43), residues: 128 sheet: -1.60 (0.40), residues: 171 loop : -2.75 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 279 HIS 0.006 0.001 HIS E 40 PHE 0.018 0.002 PHE E 389 TYR 0.022 0.002 TYR B 74 ARG 0.007 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 2.81517 ( 24) link_BETA1-4 : bond 0.00419 ( 11) link_BETA1-4 : angle 2.12319 ( 33) hydrogen bonds : bond 0.03499 ( 130) hydrogen bonds : angle 4.96902 ( 351) SS BOND : bond 0.00310 ( 13) SS BOND : angle 1.37744 ( 26) link_BETA1-3 : bond 0.00504 ( 1) link_BETA1-3 : angle 4.01116 ( 3) covalent geometry : bond 0.00334 ( 8754) covalent geometry : angle 0.75371 (11874) *********************** 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 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8207 (ptt90) REVERT: A 152 TYR cc_start: 0.7139 (t80) cc_final: 0.6785 (t80) REVERT: A 171 VAL cc_start: 0.7969 (m) cc_final: 0.7504 (t) REVERT: A 228 PHE cc_start: 0.7539 (p90) cc_final: 0.7288 (p90) REVERT: A 339 TYR cc_start: 0.7617 (p90) cc_final: 0.7330 (p90) REVERT: B 18 GLU cc_start: 0.7708 (tp30) cc_final: 0.7063 (tp30) REVERT: B 175 VAL cc_start: 0.7818 (t) cc_final: 0.7607 (p) REVERT: B 348 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6778 (tt0) REVERT: B 352 ASN cc_start: 0.8400 (m-40) cc_final: 0.8037 (m-40) REVERT: B 353 MET cc_start: 0.8025 (mmp) cc_final: 0.7387 (mmm) REVERT: B 355 VAL cc_start: 0.8112 (p) cc_final: 0.7857 (m) REVERT: E 173 ASN cc_start: 0.7694 (m-40) cc_final: 0.7425 (m-40) REVERT: E 215 VAL cc_start: 0.8721 (t) cc_final: 0.8200 (p) REVERT: E 315 LEU cc_start: 0.8042 (tp) cc_final: 0.7568 (tp) REVERT: E 317 MET cc_start: 0.6630 (mtp) cc_final: 0.6061 (mtp) REVERT: E 333 MET cc_start: 0.6674 (mmt) cc_final: 0.6439 (mmt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2443 time to fit residues: 61.8500 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158952 restraints weight = 14510.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.162857 restraints weight = 8828.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165580 restraints weight = 6105.187| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8787 Z= 0.161 Angle : 0.764 11.919 11960 Z= 0.348 Chirality : 0.046 0.259 1384 Planarity : 0.005 0.059 1497 Dihedral : 9.182 82.155 1549 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.65 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: -3.12 (0.24), residues: 1017 helix: -0.28 (0.44), residues: 128 sheet: -1.82 (0.38), residues: 183 loop : -2.68 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.008 0.001 HIS E 40 PHE 0.016 0.002 PHE B 228 TYR 0.017 0.002 TYR E 471 ARG 0.019 0.001 ARG B 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 8) link_NAG-ASN : angle 2.62412 ( 24) link_BETA1-4 : bond 0.00468 ( 11) link_BETA1-4 : angle 2.08354 ( 33) hydrogen bonds : bond 0.03380 ( 130) hydrogen bonds : angle 4.85424 ( 351) SS BOND : bond 0.00263 ( 13) SS BOND : angle 1.14126 ( 26) link_BETA1-3 : bond 0.00492 ( 1) link_BETA1-3 : angle 4.16466 ( 3) covalent geometry : bond 0.00356 ( 8754) covalent geometry : angle 0.74489 (11874) *********************** 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 187 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8236 (ptt90) REVERT: A 152 TYR cc_start: 0.7170 (t80) cc_final: 0.6794 (t80) REVERT: A 171 VAL cc_start: 0.7986 (m) cc_final: 0.7475 (t) REVERT: A 339 TYR cc_start: 0.7601 (p90) cc_final: 0.7339 (p90) REVERT: B 15 LYS cc_start: 0.8407 (tppt) cc_final: 0.8192 (tppt) REVERT: B 18 GLU cc_start: 0.7746 (tp30) cc_final: 0.7020 (tp30) REVERT: B 175 VAL cc_start: 0.7818 (t) cc_final: 0.7576 (p) REVERT: B 352 ASN cc_start: 0.8388 (m-40) cc_final: 0.8054 (m-40) REVERT: B 353 MET cc_start: 0.8019 (mmp) cc_final: 0.7428 (mmm) REVERT: B 355 VAL cc_start: 0.8150 (p) cc_final: 0.7943 (m) REVERT: E 76 GLU cc_start: 0.6718 (tt0) cc_final: 0.6498 (tt0) REVERT: E 173 ASN cc_start: 0.7683 (m-40) cc_final: 0.7445 (m-40) REVERT: E 215 VAL cc_start: 0.8641 (t) cc_final: 0.8129 (p) REVERT: E 315 LEU cc_start: 0.8147 (tp) cc_final: 0.7644 (tp) REVERT: E 317 MET cc_start: 0.6881 (mtp) cc_final: 0.6410 (mtp) REVERT: E 319 GLN cc_start: 0.8119 (mp10) cc_final: 0.7511 (mp10) REVERT: E 333 MET cc_start: 0.6603 (mmt) cc_final: 0.6387 (mmt) REVERT: E 343 GLN cc_start: 0.7818 (mt0) cc_final: 0.7572 (mt0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2408 time to fit residues: 59.1037 Evaluate side-chains 176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN E 102 ASN E 320 ASN E 368 ASN E 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159144 restraints weight = 14793.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163031 restraints weight = 8997.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165761 restraints weight = 6267.573| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8787 Z= 0.118 Angle : 0.736 12.201 11960 Z= 0.329 Chirality : 0.045 0.271 1384 Planarity : 0.005 0.057 1497 Dihedral : 8.422 78.901 1549 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -2.97 (0.24), residues: 1017 helix: -0.05 (0.45), residues: 128 sheet: -1.66 (0.39), residues: 183 loop : -2.62 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.007 0.001 HIS E 40 PHE 0.017 0.001 PHE B 228 TYR 0.025 0.001 TYR A 52 ARG 0.004 0.000 ARG E 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 2.85006 ( 24) link_BETA1-4 : bond 0.00440 ( 11) link_BETA1-4 : angle 1.93511 ( 33) hydrogen bonds : bond 0.03080 ( 130) hydrogen bonds : angle 4.63920 ( 351) SS BOND : bond 0.00171 ( 13) SS BOND : angle 1.15293 ( 26) link_BETA1-3 : bond 0.00604 ( 1) link_BETA1-3 : angle 4.30911 ( 3) covalent geometry : bond 0.00266 ( 8754) covalent geometry : angle 0.71459 (11874) *********************** 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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8185 (ptt90) REVERT: A 171 VAL cc_start: 0.7947 (m) cc_final: 0.7402 (t) REVERT: A 228 PHE cc_start: 0.7541 (p90) cc_final: 0.7327 (p90) REVERT: B 18 GLU cc_start: 0.7760 (tp30) cc_final: 0.7082 (tp30) REVERT: B 24 ILE cc_start: 0.7625 (mm) cc_final: 0.7424 (mm) REVERT: B 175 VAL cc_start: 0.7769 (t) cc_final: 0.7500 (p) REVERT: B 352 ASN cc_start: 0.8298 (m-40) cc_final: 0.7959 (m-40) REVERT: B 353 MET cc_start: 0.7989 (mmp) cc_final: 0.7448 (mmm) REVERT: B 355 VAL cc_start: 0.8106 (p) cc_final: 0.7878 (m) REVERT: E 76 GLU cc_start: 0.6555 (tt0) cc_final: 0.6136 (tt0) REVERT: E 233 GLU cc_start: 0.6701 (pp20) cc_final: 0.6312 (tm-30) REVERT: E 263 ASP cc_start: 0.7482 (m-30) cc_final: 0.6881 (m-30) REVERT: E 315 LEU cc_start: 0.8152 (tp) cc_final: 0.7622 (tp) REVERT: E 317 MET cc_start: 0.6726 (mtp) cc_final: 0.6183 (mtp) REVERT: E 319 GLN cc_start: 0.8252 (mp10) cc_final: 0.7451 (mp10) REVERT: E 320 ASN cc_start: 0.7347 (m-40) cc_final: 0.7090 (m110) REVERT: E 333 MET cc_start: 0.6649 (mmt) cc_final: 0.6398 (mmt) REVERT: E 343 GLN cc_start: 0.7805 (mt0) cc_final: 0.7383 (mt0) REVERT: E 414 ASP cc_start: 0.7235 (p0) cc_final: 0.7008 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2224 time to fit residues: 56.0344 Evaluate side-chains 175 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.0050 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 19 optimal weight: 0.0010 chunk 52 optimal weight: 0.3980 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN E 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161605 restraints weight = 15254.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.165653 restraints weight = 9171.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.168398 restraints weight = 6334.050| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8787 Z= 0.106 Angle : 0.711 12.043 11960 Z= 0.316 Chirality : 0.043 0.243 1384 Planarity : 0.005 0.049 1497 Dihedral : 7.758 75.819 1549 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.83 (0.24), residues: 1017 helix: 0.14 (0.45), residues: 129 sheet: -1.61 (0.39), residues: 184 loop : -2.52 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 166 HIS 0.007 0.001 HIS E 40 PHE 0.011 0.001 PHE B 292 TYR 0.018 0.001 TYR B 314 ARG 0.005 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 8) link_NAG-ASN : angle 2.45019 ( 24) link_BETA1-4 : bond 0.00430 ( 11) link_BETA1-4 : angle 1.81606 ( 33) hydrogen bonds : bond 0.02963 ( 130) hydrogen bonds : angle 4.58596 ( 351) SS BOND : bond 0.00532 ( 13) SS BOND : angle 1.11668 ( 26) link_BETA1-3 : bond 0.00627 ( 1) link_BETA1-3 : angle 4.38357 ( 3) covalent geometry : bond 0.00241 ( 8754) covalent geometry : angle 0.69334 (11874) *********************** 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 185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8065 (tp40) cc_final: 0.7861 (tp-100) REVERT: A 81 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8136 (ptt90) REVERT: A 171 VAL cc_start: 0.7965 (m) cc_final: 0.7405 (t) REVERT: A 228 PHE cc_start: 0.7510 (p90) cc_final: 0.7286 (p90) REVERT: A 269 LEU cc_start: 0.8149 (tt) cc_final: 0.7880 (tt) REVERT: B 18 GLU cc_start: 0.7763 (tp30) cc_final: 0.7166 (tp30) REVERT: B 352 ASN cc_start: 0.8239 (m-40) cc_final: 0.7947 (m-40) REVERT: B 353 MET cc_start: 0.7955 (mmp) cc_final: 0.7406 (mmm) REVERT: B 355 VAL cc_start: 0.8060 (p) cc_final: 0.7852 (m) REVERT: E 76 GLU cc_start: 0.6468 (tt0) cc_final: 0.6066 (tt0) REVERT: E 146 LEU cc_start: 0.8394 (mt) cc_final: 0.8137 (mt) REVERT: E 233 GLU cc_start: 0.6586 (pp20) cc_final: 0.6223 (tm-30) REVERT: E 263 ASP cc_start: 0.7381 (m-30) cc_final: 0.7007 (m-30) REVERT: E 315 LEU cc_start: 0.8100 (tp) cc_final: 0.7595 (tp) REVERT: E 317 MET cc_start: 0.6827 (mtp) cc_final: 0.6382 (mtp) REVERT: E 319 GLN cc_start: 0.8173 (mp10) cc_final: 0.7421 (mp10) REVERT: E 343 GLN cc_start: 0.7763 (mt0) cc_final: 0.7360 (mt0) REVERT: E 414 ASP cc_start: 0.7202 (p0) cc_final: 0.6940 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2317 time to fit residues: 57.0839 Evaluate side-chains 177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 0.0000 chunk 76 optimal weight: 0.0030 chunk 82 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.161414 restraints weight = 15090.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165471 restraints weight = 9015.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168215 restraints weight = 6170.219| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8787 Z= 0.102 Angle : 0.696 11.680 11960 Z= 0.309 Chirality : 0.042 0.242 1384 Planarity : 0.005 0.048 1497 Dihedral : 7.281 72.890 1549 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.78 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -2.74 (0.24), residues: 1017 helix: 0.25 (0.45), residues: 128 sheet: -1.44 (0.41), residues: 166 loop : -2.49 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 301 HIS 0.006 0.001 HIS E 40 PHE 0.020 0.001 PHE E 322 TYR 0.016 0.001 TYR B 314 ARG 0.005 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 8) link_NAG-ASN : angle 2.26082 ( 24) link_BETA1-4 : bond 0.00438 ( 11) link_BETA1-4 : angle 1.75198 ( 33) hydrogen bonds : bond 0.02959 ( 130) hydrogen bonds : angle 4.51254 ( 351) SS BOND : bond 0.00286 ( 13) SS BOND : angle 0.96418 ( 26) link_BETA1-3 : bond 0.00464 ( 1) link_BETA1-3 : angle 4.46923 ( 3) covalent geometry : bond 0.00231 ( 8754) covalent geometry : angle 0.67923 (11874) *********************** 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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8113 (tppt) cc_final: 0.7796 (ttmm) REVERT: A 81 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8094 (ptt90) REVERT: A 171 VAL cc_start: 0.7925 (m) cc_final: 0.7360 (t) REVERT: A 228 PHE cc_start: 0.7526 (p90) cc_final: 0.7305 (p90) REVERT: B 18 GLU cc_start: 0.7770 (tp30) cc_final: 0.7163 (tp30) REVERT: B 188 PHE cc_start: 0.7485 (m-80) cc_final: 0.7073 (m-80) REVERT: B 355 VAL cc_start: 0.7988 (p) cc_final: 0.7736 (m) REVERT: E 76 GLU cc_start: 0.6502 (tt0) cc_final: 0.6029 (tt0) REVERT: E 146 LEU cc_start: 0.8383 (mt) cc_final: 0.8086 (mt) REVERT: E 233 GLU cc_start: 0.6541 (pp20) cc_final: 0.6197 (tm-30) REVERT: E 263 ASP cc_start: 0.7385 (m-30) cc_final: 0.6983 (m-30) REVERT: E 315 LEU cc_start: 0.8064 (tp) cc_final: 0.7587 (tp) REVERT: E 317 MET cc_start: 0.6697 (mtp) cc_final: 0.6351 (mtp) REVERT: E 319 GLN cc_start: 0.8287 (mp10) cc_final: 0.7525 (mp10) REVERT: E 367 HIS cc_start: 0.8165 (m90) cc_final: 0.7918 (m-70) REVERT: E 414 ASP cc_start: 0.7126 (p0) cc_final: 0.6848 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2346 time to fit residues: 58.8430 Evaluate side-chains 179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 0.5980 chunk 100 optimal weight: 0.0040 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 0.0470 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN E 102 ASN E 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158531 restraints weight = 15117.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162631 restraints weight = 8852.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165467 restraints weight = 5935.492| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8787 Z= 0.115 Angle : 0.720 12.197 11960 Z= 0.318 Chirality : 0.043 0.254 1384 Planarity : 0.005 0.077 1497 Dihedral : 7.104 69.524 1549 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -2.72 (0.24), residues: 1017 helix: 0.28 (0.45), residues: 129 sheet: -1.72 (0.37), residues: 202 loop : -2.41 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.007 0.001 HIS E 40 PHE 0.018 0.001 PHE E 322 TYR 0.029 0.001 TYR B 74 ARG 0.004 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 8) link_NAG-ASN : angle 2.17751 ( 24) link_BETA1-4 : bond 0.00417 ( 11) link_BETA1-4 : angle 1.78426 ( 33) hydrogen bonds : bond 0.02972 ( 130) hydrogen bonds : angle 4.47206 ( 351) SS BOND : bond 0.00292 ( 13) SS BOND : angle 0.93533 ( 26) link_BETA1-3 : bond 0.00559 ( 1) link_BETA1-3 : angle 4.59640 ( 3) covalent geometry : bond 0.00262 ( 8754) covalent geometry : angle 0.70512 (11874) *********************** 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 185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8109 (tppt) cc_final: 0.7765 (ttmm) REVERT: A 81 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8118 (ptt90) REVERT: A 104 MET cc_start: 0.6168 (mmm) cc_final: 0.5929 (mmt) REVERT: A 171 VAL cc_start: 0.7960 (m) cc_final: 0.7410 (t) REVERT: A 339 TYR cc_start: 0.7606 (p90) cc_final: 0.7401 (p90) REVERT: B 18 GLU cc_start: 0.7822 (tp30) cc_final: 0.7186 (tp30) REVERT: B 188 PHE cc_start: 0.7554 (m-80) cc_final: 0.7153 (m-80) REVERT: B 355 VAL cc_start: 0.8085 (p) cc_final: 0.7876 (m) REVERT: E 76 GLU cc_start: 0.6532 (tt0) cc_final: 0.6010 (tt0) REVERT: E 146 LEU cc_start: 0.8371 (mt) cc_final: 0.8068 (mt) REVERT: E 212 VAL cc_start: 0.8698 (p) cc_final: 0.8455 (t) REVERT: E 233 GLU cc_start: 0.6645 (pp20) cc_final: 0.6298 (tm-30) REVERT: E 263 ASP cc_start: 0.7328 (m-30) cc_final: 0.6928 (m-30) REVERT: E 315 LEU cc_start: 0.8060 (tp) cc_final: 0.7584 (tp) REVERT: E 317 MET cc_start: 0.6860 (mtp) cc_final: 0.6397 (mtp) REVERT: E 319 GLN cc_start: 0.8164 (mp10) cc_final: 0.7439 (mp10) REVERT: E 367 HIS cc_start: 0.8181 (m90) cc_final: 0.7925 (m-70) REVERT: E 414 ASP cc_start: 0.7094 (p0) cc_final: 0.6781 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2388 time to fit residues: 58.2742 Evaluate side-chains 177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.0570 chunk 86 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157931 restraints weight = 15127.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162232 restraints weight = 8761.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165153 restraints weight = 5832.341| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8787 Z= 0.113 Angle : 0.717 12.045 11960 Z= 0.317 Chirality : 0.043 0.251 1384 Planarity : 0.005 0.070 1497 Dihedral : 6.930 66.241 1549 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.28 % Favored : 92.63 % 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: -2.70 (0.24), residues: 1017 helix: 0.41 (0.46), residues: 129 sheet: -1.73 (0.36), residues: 205 loop : -2.42 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.006 0.001 HIS E 40 PHE 0.018 0.001 PHE E 322 TYR 0.027 0.001 TYR B 74 ARG 0.006 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 8) link_NAG-ASN : angle 2.13050 ( 24) link_BETA1-4 : bond 0.00440 ( 11) link_BETA1-4 : angle 1.74201 ( 33) hydrogen bonds : bond 0.02930 ( 130) hydrogen bonds : angle 4.44938 ( 351) SS BOND : bond 0.00246 ( 13) SS BOND : angle 0.91179 ( 26) link_BETA1-3 : bond 0.00606 ( 1) link_BETA1-3 : angle 4.65358 ( 3) covalent geometry : bond 0.00260 ( 8754) covalent geometry : angle 0.70184 (11874) ********************** 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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8136 (tppt) cc_final: 0.7859 (ttmm) REVERT: A 81 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8131 (ptt90) REVERT: A 154 SER cc_start: 0.6912 (p) cc_final: 0.6335 (m) REVERT: A 171 VAL cc_start: 0.7961 (m) cc_final: 0.7407 (t) REVERT: A 269 LEU cc_start: 0.8148 (tt) cc_final: 0.7738 (tt) REVERT: A 289 HIS cc_start: 0.6565 (m170) cc_final: 0.6137 (m-70) REVERT: B 18 GLU cc_start: 0.7877 (tp30) cc_final: 0.7203 (tp30) REVERT: B 188 PHE cc_start: 0.7579 (m-80) cc_final: 0.7135 (m-80) REVERT: B 349 GLN cc_start: 0.7603 (tt0) cc_final: 0.7249 (tt0) REVERT: B 355 VAL cc_start: 0.8134 (p) cc_final: 0.7858 (m) REVERT: E 76 GLU cc_start: 0.6525 (tt0) cc_final: 0.5967 (tt0) REVERT: E 146 LEU cc_start: 0.8375 (mt) cc_final: 0.8118 (mt) REVERT: E 212 VAL cc_start: 0.8654 (p) cc_final: 0.8430 (t) REVERT: E 259 LEU cc_start: 0.8241 (tp) cc_final: 0.8016 (tt) REVERT: E 263 ASP cc_start: 0.7254 (m-30) cc_final: 0.6846 (m-30) REVERT: E 315 LEU cc_start: 0.8028 (tp) cc_final: 0.7580 (tp) REVERT: E 317 MET cc_start: 0.6973 (mtp) cc_final: 0.6498 (mtp) REVERT: E 319 GLN cc_start: 0.8191 (mp10) cc_final: 0.7413 (mp10) REVERT: E 367 HIS cc_start: 0.8161 (m90) cc_final: 0.7913 (m-70) REVERT: E 414 ASP cc_start: 0.7038 (p0) cc_final: 0.6554 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2253 time to fit residues: 56.5663 Evaluate side-chains 180 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 85 optimal weight: 0.7980 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN E 102 ASN E 149 ASN E 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161425 restraints weight = 14924.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165644 restraints weight = 8879.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168438 restraints weight = 6031.394| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8787 Z= 0.103 Angle : 0.710 11.911 11960 Z= 0.315 Chirality : 0.042 0.221 1384 Planarity : 0.005 0.066 1497 Dihedral : 6.598 61.937 1549 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.59 % Favored : 93.31 % 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: -2.62 (0.24), residues: 1017 helix: 0.43 (0.45), residues: 130 sheet: -1.57 (0.37), residues: 198 loop : -2.39 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.006 0.001 HIS E 40 PHE 0.017 0.001 PHE E 322 TYR 0.021 0.001 TYR B 74 ARG 0.006 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 8) link_NAG-ASN : angle 2.23596 ( 24) link_BETA1-4 : bond 0.00456 ( 11) link_BETA1-4 : angle 1.71431 ( 33) hydrogen bonds : bond 0.02890 ( 130) hydrogen bonds : angle 4.43047 ( 351) SS BOND : bond 0.00223 ( 13) SS BOND : angle 0.80103 ( 26) link_BETA1-3 : bond 0.00502 ( 1) link_BETA1-3 : angle 4.71222 ( 3) covalent geometry : bond 0.00234 ( 8754) covalent geometry : angle 0.69511 (11874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.49 seconds wall clock time: 52 minutes 1.69 seconds (3121.69 seconds total)