Starting phenix.real_space_refine on Sat Jul 26 15:22:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1r_33571/07_2025/7y1r_33571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1r_33571/07_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_33571/07_2025/7y1r_33571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2025/7y1r_33571.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2025/7y1r_33571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.29, 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: 2.75 Conformation dependent library (CDL) restraints added in 1.1 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: 1.03 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: 2.07 Time building geometry restraints manager: 3.01 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: 0.980 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: 0.100 Process input model: 22.590 Find NCS groups from input model: 0.250 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- 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 : 0.904 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: 0.2264 time to fit residues: 50.6776 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 : 0.928 ------------------------------------------------------------------------------- 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: 0.9980 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 = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176761 restraints weight = 15360.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180856 restraints weight = 9405.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.183695 restraints weight = 6557.721| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.946 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7897 (tp40) cc_final: 0.7545 (tp-100) REVERT: A 77 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7800 (mtpp) REVERT: A 84 MET cc_start: 0.4969 (tpt) cc_final: 0.4560 (tpt) REVERT: A 111 LEU cc_start: 0.6766 (mm) cc_final: 0.6512 (mt) REVERT: A 151 ARG cc_start: 0.7008 (ptp90) cc_final: 0.6662 (ptp90) REVERT: A 279 TRP cc_start: 0.7872 (p90) cc_final: 0.7669 (p90) REVERT: A 346 LYS cc_start: 0.8356 (pttm) cc_final: 0.7924 (pttm) REVERT: B 15 LYS cc_start: 0.8375 (tppt) cc_final: 0.7770 (tppt) REVERT: B 74 TYR cc_start: 0.6642 (t80) cc_final: 0.6387 (t80) REVERT: B 353 MET cc_start: 0.7956 (mmp) cc_final: 0.7585 (mmp) REVERT: E 90 ARG cc_start: 0.6748 (tpp-160) cc_final: 0.6402 (tpp-160) REVERT: E 319 GLN cc_start: 0.7907 (mp10) cc_final: 0.7656 (mp10) REVERT: E 414 ASP cc_start: 0.6206 (p0) cc_final: 0.5925 (p0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2212 time to fit residues: 52.1257 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 : 0.839 ------------------------------------------------------------------------------- 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: 0.4980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN E 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.183566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161935 restraints weight = 15234.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.166046 restraints weight = 9277.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.168944 restraints weight = 6471.430| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8787 Z= 0.258 Angle : 0.891 10.812 11960 Z= 0.417 Chirality : 0.050 0.278 1384 Planarity : 0.006 0.074 1497 Dihedral : 10.799 90.006 1549 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.55 % Favored : 91.35 % Rotamer: Outliers : 0.22 % Allowed : 7.24 % Favored : 92.55 % 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: -3.17 (0.23), residues: 1017 helix: -0.81 (0.42), residues: 140 sheet: -1.68 (0.39), residues: 184 loop : -2.69 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 281 HIS 0.010 0.002 HIS B 138 PHE 0.022 0.002 PHE E 314 TYR 0.028 0.003 TYR A 52 ARG 0.006 0.001 ARG E 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 8) link_NAG-ASN : angle 3.07639 ( 24) link_BETA1-4 : bond 0.00517 ( 11) link_BETA1-4 : angle 2.12500 ( 33) hydrogen bonds : bond 0.05258 ( 130) hydrogen bonds : angle 5.33551 ( 351) SS BOND : bond 0.00403 ( 13) SS BOND : angle 1.29184 ( 26) link_BETA1-3 : bond 0.00745 ( 1) link_BETA1-3 : angle 3.73539 ( 3) covalent geometry : bond 0.00563 ( 8754) covalent geometry : angle 0.87197 (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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7986 (tp40) cc_final: 0.7710 (tp40) REVERT: A 111 LEU cc_start: 0.6998 (mm) cc_final: 0.6716 (mt) REVERT: A 151 ARG cc_start: 0.7871 (ptp90) cc_final: 0.7385 (ptp90) REVERT: A 152 TYR cc_start: 0.7168 (t80) cc_final: 0.6669 (t80) REVERT: A 171 VAL cc_start: 0.7995 (m) cc_final: 0.7456 (t) REVERT: A 283 HIS cc_start: 0.7158 (m90) cc_final: 0.6810 (m90) REVERT: A 333 GLU cc_start: 0.7330 (pt0) cc_final: 0.7057 (pt0) REVERT: A 346 LYS cc_start: 0.8500 (pttm) cc_final: 0.8277 (pttp) REVERT: B 27 LYS cc_start: 0.7583 (tptt) cc_final: 0.7243 (mmmt) REVERT: B 348 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6866 (tt0) REVERT: B 349 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: B 353 MET cc_start: 0.8019 (mmp) cc_final: 0.7301 (mmm) REVERT: B 355 VAL cc_start: 0.8057 (p) cc_final: 0.7773 (m) REVERT: B 359 LYS cc_start: 0.7568 (ptpp) cc_final: 0.7356 (ptpp) REVERT: E 90 ARG cc_start: 0.6727 (tpp-160) cc_final: 0.6436 (tpp-160) REVERT: E 215 VAL cc_start: 0.8733 (t) cc_final: 0.8244 (p) REVERT: E 315 LEU cc_start: 0.8172 (tp) cc_final: 0.7689 (tp) REVERT: E 317 MET cc_start: 0.7098 (mtp) cc_final: 0.6438 (mtp) REVERT: E 319 GLN cc_start: 0.7834 (mp10) cc_final: 0.7441 (mp10) REVERT: E 389 PHE cc_start: 0.7644 (t80) cc_final: 0.7233 (t80) outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.2145 time to fit residues: 54.1388 Evaluate side-chains 181 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 0.0270 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163921 restraints weight = 15162.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.167833 restraints weight = 9248.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170574 restraints weight = 6503.185| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8787 Z= 0.139 Angle : 0.738 11.770 11960 Z= 0.328 Chirality : 0.044 0.261 1384 Planarity : 0.005 0.068 1497 Dihedral : 9.350 85.208 1549 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.78 % Favored : 93.12 % 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: -2.91 (0.24), residues: 1017 helix: -0.19 (0.43), residues: 134 sheet: -1.45 (0.41), residues: 175 loop : -2.60 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 281 HIS 0.006 0.001 HIS E 40 PHE 0.018 0.002 PHE A 228 TYR 0.024 0.002 TYR B 74 ARG 0.008 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 8) link_NAG-ASN : angle 2.53772 ( 24) link_BETA1-4 : bond 0.00455 ( 11) link_BETA1-4 : angle 2.06440 ( 33) hydrogen bonds : bond 0.03077 ( 130) hydrogen bonds : angle 4.72414 ( 351) SS BOND : bond 0.00785 ( 13) SS BOND : angle 0.96023 ( 26) link_BETA1-3 : bond 0.00610 ( 1) link_BETA1-3 : angle 3.96257 ( 3) covalent geometry : bond 0.00314 ( 8754) covalent geometry : angle 0.71938 (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 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8027 (tp40) cc_final: 0.7736 (tp40) REVERT: A 81 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8156 (ptt90) REVERT: A 84 MET cc_start: 0.5361 (tpt) cc_final: 0.4948 (tpt) REVERT: A 111 LEU cc_start: 0.7100 (mm) cc_final: 0.6884 (mt) REVERT: A 151 ARG cc_start: 0.7878 (ptp90) cc_final: 0.7509 (ptp90) REVERT: A 152 TYR cc_start: 0.7042 (t80) cc_final: 0.6627 (t80) REVERT: A 171 VAL cc_start: 0.7996 (m) cc_final: 0.7438 (t) REVERT: A 333 GLU cc_start: 0.7502 (pt0) cc_final: 0.7070 (pt0) REVERT: B 15 LYS cc_start: 0.8374 (tppt) cc_final: 0.8130 (tppt) REVERT: B 348 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6814 (tt0) REVERT: B 353 MET cc_start: 0.8000 (mmp) cc_final: 0.7407 (mmm) REVERT: B 355 VAL cc_start: 0.7981 (p) cc_final: 0.7774 (m) REVERT: E 90 ARG cc_start: 0.6812 (tpp-160) cc_final: 0.6421 (tpp-160) REVERT: E 215 VAL cc_start: 0.8632 (t) cc_final: 0.8122 (p) REVERT: E 233 GLU cc_start: 0.6568 (pp20) cc_final: 0.6213 (tm-30) REVERT: E 315 LEU cc_start: 0.8127 (tp) cc_final: 0.7717 (tp) REVERT: E 317 MET cc_start: 0.6674 (mtp) cc_final: 0.6444 (mtp) REVERT: E 319 GLN cc_start: 0.8179 (mp10) cc_final: 0.7465 (mp10) REVERT: E 333 MET cc_start: 0.6468 (mmt) cc_final: 0.6121 (mmm) REVERT: E 389 PHE cc_start: 0.7529 (t80) cc_final: 0.7086 (t80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2254 time to fit residues: 55.1443 Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 0.0770 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.184707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163811 restraints weight = 15136.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.167825 restraints weight = 9237.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170580 restraints weight = 6471.999| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.4178 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= 0.118 Angle : 0.708 11.265 11960 Z= 0.316 Chirality : 0.043 0.258 1384 Planarity : 0.005 0.055 1497 Dihedral : 8.690 82.591 1549 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -2.84 (0.24), residues: 1017 helix: -0.01 (0.44), residues: 134 sheet: -1.45 (0.41), residues: 176 loop : -2.57 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 281 HIS 0.006 0.001 HIS E 40 PHE 0.016 0.001 PHE A 228 TYR 0.020 0.001 TYR B 314 ARG 0.003 0.000 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 8) link_NAG-ASN : angle 2.32465 ( 24) link_BETA1-4 : bond 0.00448 ( 11) link_BETA1-4 : angle 1.88279 ( 33) hydrogen bonds : bond 0.02898 ( 130) hydrogen bonds : angle 4.63801 ( 351) SS BOND : bond 0.00764 ( 13) SS BOND : angle 1.40751 ( 26) link_BETA1-3 : bond 0.00627 ( 1) link_BETA1-3 : angle 4.04713 ( 3) covalent geometry : bond 0.00264 ( 8754) covalent geometry : angle 0.68927 (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 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7859 (tp40) cc_final: 0.7611 (tp40) REVERT: A 81 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8127 (ptt90) REVERT: A 84 MET cc_start: 0.5419 (tpt) cc_final: 0.4852 (tpt) REVERT: A 151 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7625 (ptp90) REVERT: A 152 TYR cc_start: 0.7051 (t80) cc_final: 0.6734 (t80) REVERT: A 171 VAL cc_start: 0.8010 (m) cc_final: 0.7402 (t) REVERT: A 333 GLU cc_start: 0.7440 (pt0) cc_final: 0.7135 (pt0) REVERT: B 299 TYR cc_start: 0.7367 (t80) cc_final: 0.7128 (t80) REVERT: B 348 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6823 (tt0) REVERT: B 353 MET cc_start: 0.7953 (mmp) cc_final: 0.7354 (mmm) REVERT: E 90 ARG cc_start: 0.6879 (tpp-160) cc_final: 0.6485 (tpp-160) REVERT: E 315 LEU cc_start: 0.8116 (tp) cc_final: 0.7648 (tp) REVERT: E 318 SER cc_start: 0.7596 (p) cc_final: 0.7274 (p) REVERT: E 325 LEU cc_start: 0.7042 (tt) cc_final: 0.6433 (mp) REVERT: E 333 MET cc_start: 0.6611 (mmt) cc_final: 0.6298 (mmm) REVERT: E 389 PHE cc_start: 0.7522 (t80) cc_final: 0.7089 (t80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2343 time to fit residues: 57.1607 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 : 0.871 ------------------------------------------------------------------------------- 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: 0.3980 chunk 48 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162974 restraints weight = 14939.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.166935 restraints weight = 9132.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.169686 restraints weight = 6391.114| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8787 Z= 0.129 Angle : 0.727 11.234 11960 Z= 0.324 Chirality : 0.044 0.262 1384 Planarity : 0.005 0.052 1497 Dihedral : 8.157 78.852 1549 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.57 % Favored : 92.33 % 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: -2.82 (0.24), residues: 1017 helix: 0.26 (0.45), residues: 128 sheet: -1.54 (0.40), residues: 176 loop : -2.56 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 281 HIS 0.006 0.001 HIS E 40 PHE 0.018 0.001 PHE A 228 TYR 0.025 0.002 TYR A 52 ARG 0.005 0.000 ARG B 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 8) link_NAG-ASN : angle 2.61353 ( 24) link_BETA1-4 : bond 0.00513 ( 11) link_BETA1-4 : angle 1.86119 ( 33) hydrogen bonds : bond 0.03009 ( 130) hydrogen bonds : angle 4.60996 ( 351) SS BOND : bond 0.00213 ( 13) SS BOND : angle 1.15122 ( 26) link_BETA1-3 : bond 0.01054 ( 1) link_BETA1-3 : angle 4.28694 ( 3) covalent geometry : bond 0.00291 ( 8754) covalent geometry : angle 0.70859 (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 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7911 (tp40) cc_final: 0.7618 (tp40) REVERT: A 81 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8139 (ptt90) REVERT: A 104 MET cc_start: 0.6594 (mmm) cc_final: 0.6380 (mmt) REVERT: A 151 ARG cc_start: 0.7921 (ptp90) cc_final: 0.7708 (ptp90) REVERT: A 152 TYR cc_start: 0.7093 (t80) cc_final: 0.6785 (t80) REVERT: A 171 VAL cc_start: 0.8037 (m) cc_final: 0.7446 (t) REVERT: A 333 GLU cc_start: 0.7545 (pt0) cc_final: 0.7219 (pt0) REVERT: B 291 ASN cc_start: 0.8033 (m110) cc_final: 0.7818 (m-40) REVERT: B 348 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6831 (tt0) REVERT: B 353 MET cc_start: 0.7943 (mmp) cc_final: 0.7373 (mmm) REVERT: E 76 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6459 (tp30) REVERT: E 90 ARG cc_start: 0.6886 (tpp-160) cc_final: 0.6432 (tpp-160) REVERT: E 116 LEU cc_start: 0.7449 (mm) cc_final: 0.7201 (mm) REVERT: E 212 VAL cc_start: 0.8677 (p) cc_final: 0.8437 (t) REVERT: E 238 ASP cc_start: 0.7654 (t0) cc_final: 0.7402 (t0) REVERT: E 315 LEU cc_start: 0.8046 (tp) cc_final: 0.7583 (tp) REVERT: E 317 MET cc_start: 0.6700 (mtp) cc_final: 0.6212 (mtp) REVERT: E 318 SER cc_start: 0.7686 (p) cc_final: 0.6860 (p) REVERT: E 333 MET cc_start: 0.6630 (mmt) cc_final: 0.6418 (mmt) REVERT: E 343 GLN cc_start: 0.7572 (mt0) cc_final: 0.7334 (mt0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2446 time to fit residues: 59.1555 Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 0.0870 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS 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 = 0.4292 r_free = 0.4292 target = 0.182558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.161926 restraints weight = 15173.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165930 restraints weight = 9239.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168672 restraints weight = 6425.028| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8787 Z= 0.125 Angle : 0.725 11.545 11960 Z= 0.322 Chirality : 0.044 0.258 1384 Planarity : 0.005 0.048 1497 Dihedral : 7.688 76.007 1549 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -2.82 (0.24), residues: 1017 helix: 0.30 (0.46), residues: 128 sheet: -1.62 (0.40), residues: 176 loop : -2.54 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 281 HIS 0.006 0.001 HIS E 191 PHE 0.016 0.001 PHE A 228 TYR 0.032 0.002 TYR B 74 ARG 0.006 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 8) link_NAG-ASN : angle 2.33594 ( 24) link_BETA1-4 : bond 0.00418 ( 11) link_BETA1-4 : angle 1.81082 ( 33) hydrogen bonds : bond 0.02952 ( 130) hydrogen bonds : angle 4.50327 ( 351) SS BOND : bond 0.00147 ( 13) SS BOND : angle 0.93772 ( 26) link_BETA1-3 : bond 0.00560 ( 1) link_BETA1-3 : angle 4.32462 ( 3) covalent geometry : bond 0.00282 ( 8754) covalent geometry : angle 0.70925 (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 186 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7905 (tp40) cc_final: 0.7598 (tp40) REVERT: A 81 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8132 (ptt90) REVERT: A 152 TYR cc_start: 0.7104 (t80) cc_final: 0.6771 (t80) REVERT: A 171 VAL cc_start: 0.7902 (m) cc_final: 0.7371 (t) REVERT: A 333 GLU cc_start: 0.7669 (pt0) cc_final: 0.7219 (pt0) REVERT: A 347 VAL cc_start: 0.8866 (p) cc_final: 0.8536 (m) REVERT: B 18 GLU cc_start: 0.7793 (tp30) cc_final: 0.7282 (tp30) REVERT: B 228 PHE cc_start: 0.5918 (m-10) cc_final: 0.4975 (m-10) REVERT: B 348 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6816 (tt0) REVERT: B 349 GLN cc_start: 0.7433 (tt0) cc_final: 0.7172 (tt0) REVERT: B 353 MET cc_start: 0.7920 (mmp) cc_final: 0.7370 (mmm) REVERT: E 90 ARG cc_start: 0.6916 (tpp-160) cc_final: 0.6480 (tpp-160) REVERT: E 315 LEU cc_start: 0.8080 (tp) cc_final: 0.7588 (tp) REVERT: E 317 MET cc_start: 0.6643 (mtp) cc_final: 0.6240 (mtp) REVERT: E 318 SER cc_start: 0.7612 (p) cc_final: 0.6938 (p) REVERT: E 343 GLN cc_start: 0.7629 (mt0) cc_final: 0.7348 (mt0) REVERT: E 414 ASP cc_start: 0.7114 (p0) cc_final: 0.6895 (p0) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2561 time to fit residues: 62.5606 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 : 0.951 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155392 restraints weight = 14673.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159369 restraints weight = 8820.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162126 restraints weight = 6018.050| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8787 Z= 0.209 Angle : 0.855 13.001 11960 Z= 0.396 Chirality : 0.050 0.279 1384 Planarity : 0.006 0.082 1497 Dihedral : 8.228 73.117 1549 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.13 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -2.98 (0.24), residues: 1017 helix: 0.09 (0.45), residues: 129 sheet: -1.75 (0.36), residues: 207 loop : -2.64 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 178 HIS 0.008 0.002 HIS E 40 PHE 0.022 0.002 PHE B 228 TYR 0.033 0.003 TYR B 74 ARG 0.008 0.001 ARG B 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.68739 ( 24) link_BETA1-4 : bond 0.00432 ( 11) link_BETA1-4 : angle 2.08815 ( 33) hydrogen bonds : bond 0.03865 ( 130) hydrogen bonds : angle 4.95457 ( 351) SS BOND : bond 0.00520 ( 13) SS BOND : angle 1.32034 ( 26) link_BETA1-3 : bond 0.00232 ( 1) link_BETA1-3 : angle 4.65023 ( 3) covalent geometry : bond 0.00459 ( 8754) covalent geometry : angle 0.83668 (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 212 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6728 (tp30) cc_final: 0.6325 (tp30) REVERT: A 52 TYR cc_start: 0.7250 (t80) cc_final: 0.7018 (t80) REVERT: A 81 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8184 (ptt90) REVERT: A 104 MET cc_start: 0.5463 (mmt) cc_final: 0.5056 (mmm) REVERT: A 171 VAL cc_start: 0.8066 (m) cc_final: 0.7583 (t) REVERT: A 279 TRP cc_start: 0.8007 (p90) cc_final: 0.7759 (p90) REVERT: A 333 GLU cc_start: 0.7873 (pt0) cc_final: 0.7458 (mt-10) REVERT: B 18 GLU cc_start: 0.7794 (tp30) cc_final: 0.7107 (tp30) REVERT: B 27 LYS cc_start: 0.7986 (tptt) cc_final: 0.7565 (tptt) REVERT: B 74 TYR cc_start: 0.8049 (t80) cc_final: 0.7775 (t80) REVERT: B 78 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6955 (tm-30) REVERT: B 175 VAL cc_start: 0.7784 (t) cc_final: 0.7485 (p) REVERT: B 349 GLN cc_start: 0.7388 (tt0) cc_final: 0.7101 (tt0) REVERT: B 353 MET cc_start: 0.7980 (mmp) cc_final: 0.7764 (mmm) REVERT: E 143 SER cc_start: 0.7587 (m) cc_final: 0.7044 (p) REVERT: E 149 ASN cc_start: 0.8222 (m-40) cc_final: 0.7836 (m-40) REVERT: E 215 VAL cc_start: 0.8672 (t) cc_final: 0.8081 (p) REVERT: E 238 ASP cc_start: 0.7812 (t0) cc_final: 0.7608 (t0) REVERT: E 315 LEU cc_start: 0.8043 (tp) cc_final: 0.7578 (tp) REVERT: E 317 MET cc_start: 0.7014 (mtp) cc_final: 0.6305 (mtp) REVERT: E 318 SER cc_start: 0.7746 (p) cc_final: 0.7122 (p) REVERT: E 341 LEU cc_start: 0.8095 (mt) cc_final: 0.7884 (mt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2294 time to fit residues: 65.0316 Evaluate side-chains 197 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 23 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.158179 restraints weight = 14748.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162191 restraints weight = 8851.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.164990 restraints weight = 6064.770| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8787 Z= 0.121 Angle : 0.760 13.172 11960 Z= 0.343 Chirality : 0.044 0.229 1384 Planarity : 0.005 0.079 1497 Dihedral : 7.569 69.749 1549 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.55 % Favored : 91.35 % 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: -2.83 (0.24), residues: 1017 helix: 0.35 (0.46), residues: 129 sheet: -1.63 (0.38), residues: 189 loop : -2.57 (0.20), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 281 HIS 0.007 0.001 HIS E 40 PHE 0.016 0.001 PHE B 188 TYR 0.032 0.002 TYR B 74 ARG 0.005 0.000 ARG B 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 2.27075 ( 24) link_BETA1-4 : bond 0.00479 ( 11) link_BETA1-4 : angle 1.76133 ( 33) hydrogen bonds : bond 0.03097 ( 130) hydrogen bonds : angle 4.69707 ( 351) SS BOND : bond 0.00220 ( 13) SS BOND : angle 1.37489 ( 26) link_BETA1-3 : bond 0.00570 ( 1) link_BETA1-3 : angle 4.54275 ( 3) covalent geometry : bond 0.00277 ( 8754) covalent geometry : angle 0.74370 (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 192 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8127 (ptt90) REVERT: A 104 MET cc_start: 0.5440 (mmt) cc_final: 0.5022 (mmm) REVERT: A 154 SER cc_start: 0.6864 (p) cc_final: 0.6318 (m) REVERT: A 171 VAL cc_start: 0.8003 (m) cc_final: 0.7535 (t) REVERT: A 228 PHE cc_start: 0.7545 (p90) cc_final: 0.7337 (p90) REVERT: A 333 GLU cc_start: 0.7907 (pt0) cc_final: 0.7500 (mt-10) REVERT: B 18 GLU cc_start: 0.7793 (tp30) cc_final: 0.7152 (tp30) REVERT: B 78 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6787 (tm-30) REVERT: B 175 VAL cc_start: 0.7707 (t) cc_final: 0.7397 (p) REVERT: B 292 PHE cc_start: 0.7173 (p90) cc_final: 0.6757 (p90) REVERT: B 353 MET cc_start: 0.7873 (mmp) cc_final: 0.7423 (mmm) REVERT: E 90 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.7007 (tpp-160) REVERT: E 116 LEU cc_start: 0.7604 (mm) cc_final: 0.7377 (mm) REVERT: E 149 ASN cc_start: 0.8144 (m-40) cc_final: 0.7600 (m-40) REVERT: E 263 ASP cc_start: 0.7238 (m-30) cc_final: 0.6780 (m-30) REVERT: E 315 LEU cc_start: 0.7986 (tp) cc_final: 0.7503 (tp) REVERT: E 317 MET cc_start: 0.6931 (mtp) cc_final: 0.6435 (mtp) REVERT: E 318 SER cc_start: 0.7714 (p) cc_final: 0.7233 (p) REVERT: E 319 GLN cc_start: 0.8103 (mp10) cc_final: 0.7530 (mt0) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2330 time to fit residues: 59.4890 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156868 restraints weight = 14523.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160879 restraints weight = 8730.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163628 restraints weight = 5965.972| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8787 Z= 0.148 Angle : 0.776 12.848 11960 Z= 0.354 Chirality : 0.045 0.239 1384 Planarity : 0.005 0.068 1497 Dihedral : 7.466 65.831 1549 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.46 % 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: -2.97 (0.24), residues: 1017 helix: 0.20 (0.45), residues: 129 sheet: -1.82 (0.37), residues: 194 loop : -2.63 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 281 HIS 0.008 0.001 HIS E 342 PHE 0.014 0.001 PHE E 322 TYR 0.049 0.002 TYR A 52 ARG 0.007 0.000 ARG B 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.52241 ( 24) link_BETA1-4 : bond 0.00484 ( 11) link_BETA1-4 : angle 1.95122 ( 33) hydrogen bonds : bond 0.03529 ( 130) hydrogen bonds : angle 4.77097 ( 351) SS BOND : bond 0.00245 ( 13) SS BOND : angle 1.47438 ( 26) link_BETA1-3 : bond 0.00409 ( 1) link_BETA1-3 : angle 4.74083 ( 3) covalent geometry : bond 0.00331 ( 8754) covalent geometry : angle 0.75681 (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 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6654 (tp30) cc_final: 0.6250 (tp30) REVERT: A 81 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8176 (ptt90) REVERT: A 104 MET cc_start: 0.5568 (mmt) cc_final: 0.5123 (mmm) REVERT: A 154 SER cc_start: 0.7061 (p) cc_final: 0.6664 (m) REVERT: A 171 VAL cc_start: 0.8085 (m) cc_final: 0.7643 (t) REVERT: A 193 HIS cc_start: 0.4167 (t-90) cc_final: 0.3956 (t-170) REVERT: A 347 VAL cc_start: 0.8813 (p) cc_final: 0.8504 (m) REVERT: B 18 GLU cc_start: 0.7755 (tp30) cc_final: 0.7120 (tp30) REVERT: B 24 ILE cc_start: 0.7832 (mm) cc_final: 0.7421 (mt) REVERT: B 175 VAL cc_start: 0.7736 (t) cc_final: 0.7426 (p) REVERT: B 292 PHE cc_start: 0.7145 (p90) cc_final: 0.6798 (p90) REVERT: B 353 MET cc_start: 0.7914 (mmp) cc_final: 0.7513 (mmm) REVERT: E 149 ASN cc_start: 0.8117 (m-40) cc_final: 0.7641 (m-40) REVERT: E 212 VAL cc_start: 0.8642 (p) cc_final: 0.8431 (t) REVERT: E 315 LEU cc_start: 0.8070 (tp) cc_final: 0.7547 (tp) REVERT: E 317 MET cc_start: 0.7068 (mtp) cc_final: 0.6434 (mtp) REVERT: E 318 SER cc_start: 0.7823 (p) cc_final: 0.7266 (p) REVERT: E 347 MET cc_start: 0.4641 (tmm) cc_final: 0.3953 (tmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2194 time to fit residues: 59.3263 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 : 0.878 ------------------------------------------------------------------------------- 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: 0.8980 chunk 69 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156073 restraints weight = 14652.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.160113 restraints weight = 8793.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162830 restraints weight = 6021.696| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8787 Z= 0.143 Angle : 0.780 13.150 11960 Z= 0.352 Chirality : 0.044 0.224 1384 Planarity : 0.005 0.066 1497 Dihedral : 7.376 62.532 1549 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.64 % Favored : 90.27 % 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: -2.90 (0.24), residues: 1017 helix: 0.23 (0.44), residues: 129 sheet: -1.74 (0.36), residues: 198 loop : -2.59 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 281 HIS 0.009 0.001 HIS E 342 PHE 0.019 0.002 PHE E 322 TYR 0.033 0.002 TYR B 74 ARG 0.007 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 8) link_NAG-ASN : angle 2.90743 ( 24) link_BETA1-4 : bond 0.00449 ( 11) link_BETA1-4 : angle 1.92672 ( 33) hydrogen bonds : bond 0.03379 ( 130) hydrogen bonds : angle 4.69894 ( 351) SS BOND : bond 0.00209 ( 13) SS BOND : angle 1.26058 ( 26) link_BETA1-3 : bond 0.00494 ( 1) link_BETA1-3 : angle 4.79854 ( 3) covalent geometry : bond 0.00326 ( 8754) covalent geometry : angle 0.75897 (11874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.18 seconds wall clock time: 52 minutes 20.08 seconds (3140.08 seconds total)