Starting phenix.real_space_refine on Wed Feb 4 03:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1r_33571/02_2026/7y1r_33571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1r_33571/02_2026/7y1r_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_33571/02_2026/7y1r_33571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1r_33571/02_2026/7y1r_33571.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1r_33571/02_2026/7y1r_33571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1r_33571/02_2026/7y1r_33571.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 2.07, per 1000 atoms: 0.24 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: 0.83 Conformation dependent library (CDL) restraints added in 336.4 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 19 sheets defined 16.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 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: 1.13 Time building geometry restraints manager: 1.06 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: 1.310 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG A 189 TYR 0.023 0.001 TYR B 74 PHE 0.012 0.001 PHE A 257 TRP 0.051 0.002 TRP A 281 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8754) covalent geometry : angle 0.70418 (11874) SS BOND : bond 0.00129 ( 13) SS BOND : angle 0.77790 ( 26) hydrogen bonds : bond 0.22318 ( 130) hydrogen bonds : angle 7.91424 ( 351) link_BETA1-3 : bond 0.01056 ( 1) link_BETA1-3 : angle 1.71039 ( 3) link_BETA1-4 : bond 0.00397 ( 11) link_BETA1-4 : angle 1.37530 ( 33) link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 1.84553 ( 24) *********************** 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 : 0.307 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: 0.7258 (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: 0.6759 (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: 0.0999 time to fit residues: 22.5003 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN E 343 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.196809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.175742 restraints weight = 15490.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179869 restraints weight = 9492.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182766 restraints weight = 6608.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184546 restraints weight = 5008.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.186096 restraints weight = 4093.179| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8787 Z= 0.157 Angle : 0.750 9.455 11960 Z= 0.334 Chirality : 0.046 0.317 1384 Planarity : 0.005 0.082 1497 Dihedral : 10.992 93.272 1549 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.24), residues: 1017 helix: 0.08 (0.45), residues: 128 sheet: -1.49 (0.44), residues: 148 loop : -2.53 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 127 TYR 0.017 0.002 TYR A 152 PHE 0.012 0.002 PHE E 389 TRP 0.024 0.002 TRP A 281 HIS 0.009 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8754) covalent geometry : angle 0.72323 (11874) SS BOND : bond 0.00289 ( 13) SS BOND : angle 1.06426 ( 26) hydrogen bonds : bond 0.03240 ( 130) hydrogen bonds : angle 5.13122 ( 351) link_BETA1-3 : bond 0.00600 ( 1) link_BETA1-3 : angle 3.73743 ( 3) link_BETA1-4 : bond 0.00579 ( 11) link_BETA1-4 : angle 3.12647 ( 33) link_NAG-ASN : bond 0.00457 ( 8) link_NAG-ASN : angle 2.17676 ( 24) *********************** 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 175 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7890 (tp40) cc_final: 0.7540 (tp-100) REVERT: A 84 MET cc_start: 0.4822 (tpt) cc_final: 0.4406 (tpt) REVERT: A 111 LEU cc_start: 0.6803 (mm) cc_final: 0.6545 (mt) REVERT: A 151 ARG cc_start: 0.7101 (ptp90) cc_final: 0.6734 (ptp90) REVERT: A 279 TRP cc_start: 0.7942 (p90) cc_final: 0.7551 (p90) REVERT: A 339 TYR cc_start: 0.6911 (p90) cc_final: 0.6710 (p90) REVERT: A 346 LYS cc_start: 0.8379 (pttm) cc_final: 0.7968 (pttm) REVERT: B 15 LYS cc_start: 0.8371 (tppt) cc_final: 0.7782 (tppt) REVERT: B 74 TYR cc_start: 0.6584 (t80) cc_final: 0.6365 (t80) REVERT: B 353 MET cc_start: 0.8019 (mmp) cc_final: 0.7637 (mmp) REVERT: E 319 GLN cc_start: 0.7935 (mp10) cc_final: 0.7655 (mp10) REVERT: E 414 ASP cc_start: 0.6273 (p0) cc_final: 0.5977 (p0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0907 time to fit residues: 21.6956 Evaluate side-chains 160 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.0470 chunk 24 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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 B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.196547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175881 restraints weight = 15417.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179910 restraints weight = 9524.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182765 restraints weight = 6656.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.184567 restraints weight = 5045.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186046 restraints weight = 4134.944| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8787 Z= 0.110 Angle : 0.663 9.486 11960 Z= 0.292 Chirality : 0.043 0.235 1384 Planarity : 0.004 0.064 1497 Dihedral : 9.809 89.472 1549 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.24), residues: 1017 helix: -0.10 (0.43), residues: 140 sheet: -1.72 (0.42), residues: 165 loop : -2.43 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 153 TYR 0.021 0.001 TYR B 314 PHE 0.009 0.001 PHE B 228 TRP 0.027 0.002 TRP A 281 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8754) covalent geometry : angle 0.64407 (11874) SS BOND : bond 0.00254 ( 13) SS BOND : angle 0.92883 ( 26) hydrogen bonds : bond 0.03534 ( 130) hydrogen bonds : angle 4.90838 ( 351) link_BETA1-3 : bond 0.00822 ( 1) link_BETA1-3 : angle 3.65379 ( 3) link_BETA1-4 : bond 0.00390 ( 11) link_BETA1-4 : angle 2.17413 ( 33) link_NAG-ASN : bond 0.00310 ( 8) link_NAG-ASN : angle 2.13730 ( 24) *********************** 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 175 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.4878 (tpt) cc_final: 0.4468 (tpt) REVERT: A 151 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6784 (ptp90) REVERT: A 171 VAL cc_start: 0.7827 (m) cc_final: 0.7186 (t) REVERT: A 289 HIS cc_start: 0.6458 (m-70) cc_final: 0.6152 (m-70) REVERT: A 333 GLU cc_start: 0.6369 (pt0) cc_final: 0.6136 (pt0) REVERT: B 18 GLU cc_start: 0.7806 (tp30) cc_final: 0.7533 (tp30) REVERT: B 27 LYS cc_start: 0.6973 (tptt) cc_final: 0.6758 (tppp) REVERT: B 349 GLN cc_start: 0.7387 (tt0) cc_final: 0.7107 (tt0) REVERT: E 208 THR cc_start: 0.6571 (t) cc_final: 0.6103 (t) REVERT: E 315 LEU cc_start: 0.7944 (tp) cc_final: 0.7664 (tp) REVERT: E 319 GLN cc_start: 0.7967 (mp10) cc_final: 0.7626 (mp10) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1014 time to fit residues: 23.8723 Evaluate side-chains 163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** B 23 GLN B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.191353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.169947 restraints weight = 15668.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.174185 restraints weight = 9455.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177072 restraints weight = 6532.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179074 restraints weight = 4939.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180330 restraints weight = 3985.112| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.2867 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= 0.123 Angle : 0.679 9.763 11960 Z= 0.300 Chirality : 0.043 0.271 1384 Planarity : 0.004 0.056 1497 Dihedral : 8.584 84.654 1549 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.24), residues: 1017 helix: 0.10 (0.44), residues: 134 sheet: -1.64 (0.43), residues: 160 loop : -2.44 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 190 TYR 0.013 0.001 TYR B 314 PHE 0.008 0.001 PHE A 228 TRP 0.026 0.002 TRP A 281 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8754) covalent geometry : angle 0.66326 (11874) SS BOND : bond 0.00242 ( 13) SS BOND : angle 0.87588 ( 26) hydrogen bonds : bond 0.02873 ( 130) hydrogen bonds : angle 4.53784 ( 351) link_BETA1-3 : bond 0.00645 ( 1) link_BETA1-3 : angle 3.99150 ( 3) link_BETA1-4 : bond 0.00480 ( 11) link_BETA1-4 : angle 1.87454 ( 33) link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 2.06075 ( 24) *********************** 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 185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8260 (ttp80) cc_final: 0.8003 (ptt90) REVERT: A 84 MET cc_start: 0.4806 (tpt) cc_final: 0.4444 (tpt) REVERT: A 151 ARG cc_start: 0.7646 (ptp90) cc_final: 0.7315 (ptp90) REVERT: A 152 TYR cc_start: 0.6897 (t80) cc_final: 0.6493 (t80) REVERT: A 171 VAL cc_start: 0.7921 (m) cc_final: 0.7261 (t) REVERT: A 333 GLU cc_start: 0.6842 (pt0) cc_final: 0.6638 (pt0) REVERT: A 338 VAL cc_start: 0.7705 (t) cc_final: 0.7329 (p) REVERT: A 346 LYS cc_start: 0.8435 (pttm) cc_final: 0.8182 (pttp) REVERT: B 301 TRP cc_start: 0.7487 (m100) cc_final: 0.7203 (m100) REVERT: B 355 VAL cc_start: 0.7485 (p) cc_final: 0.7049 (m) REVERT: E 263 ASP cc_start: 0.7583 (m-30) cc_final: 0.7200 (m-30) REVERT: E 315 LEU cc_start: 0.8140 (tp) cc_final: 0.7667 (tp) REVERT: E 317 MET cc_start: 0.6649 (mtp) cc_final: 0.6379 (mtm) REVERT: E 319 GLN cc_start: 0.7874 (mp10) cc_final: 0.7529 (mp10) REVERT: E 325 LEU cc_start: 0.6859 (tt) cc_final: 0.6142 (mm) REVERT: E 415 MET cc_start: 0.5964 (pmm) cc_final: 0.5660 (pmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0960 time to fit residues: 24.1920 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.6612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.187808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167024 restraints weight = 15268.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171151 restraints weight = 9297.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.173952 restraints weight = 6447.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175967 restraints weight = 4882.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177367 restraints weight = 3924.759| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8787 Z= 0.135 Angle : 0.702 9.648 11960 Z= 0.314 Chirality : 0.043 0.258 1384 Planarity : 0.005 0.048 1497 Dihedral : 8.280 81.701 1549 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.19 % Favored : 93.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.24), residues: 1017 helix: 0.19 (0.44), residues: 138 sheet: -1.39 (0.44), residues: 155 loop : -2.57 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 153 TYR 0.019 0.001 TYR B 270 PHE 0.018 0.001 PHE E 389 TRP 0.016 0.001 TRP A 279 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8754) covalent geometry : angle 0.68818 (11874) SS BOND : bond 0.00474 ( 13) SS BOND : angle 0.93694 ( 26) hydrogen bonds : bond 0.02892 ( 130) hydrogen bonds : angle 4.43569 ( 351) link_BETA1-3 : bond 0.00688 ( 1) link_BETA1-3 : angle 3.99562 ( 3) link_BETA1-4 : bond 0.00445 ( 11) link_BETA1-4 : angle 1.77637 ( 33) link_NAG-ASN : bond 0.00277 ( 8) link_NAG-ASN : angle 2.07281 ( 24) *********************** 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 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8137 (ptt90) REVERT: A 84 MET cc_start: 0.5057 (tpt) cc_final: 0.4597 (tpt) REVERT: A 151 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7560 (ptp90) REVERT: A 152 TYR cc_start: 0.7008 (t80) cc_final: 0.6583 (t80) REVERT: A 171 VAL cc_start: 0.7834 (m) cc_final: 0.7214 (t) REVERT: A 283 HIS cc_start: 0.6488 (m90) cc_final: 0.6205 (m90) REVERT: A 333 GLU cc_start: 0.7192 (pt0) cc_final: 0.6876 (pt0) REVERT: A 338 VAL cc_start: 0.7895 (t) cc_final: 0.7480 (p) REVERT: A 346 LYS cc_start: 0.8439 (pttm) cc_final: 0.8176 (pttp) REVERT: B 224 MET cc_start: 0.4267 (mpp) cc_final: 0.3843 (mpp) REVERT: B 301 TRP cc_start: 0.7574 (m100) cc_final: 0.7255 (m100) REVERT: E 263 ASP cc_start: 0.7611 (m-30) cc_final: 0.6902 (m-30) REVERT: E 315 LEU cc_start: 0.8121 (tp) cc_final: 0.7660 (tp) REVERT: E 317 MET cc_start: 0.6904 (mtp) cc_final: 0.6617 (mtp) REVERT: E 319 GLN cc_start: 0.8104 (mp10) cc_final: 0.7289 (mp10) REVERT: E 343 GLN cc_start: 0.7795 (mt0) cc_final: 0.7227 (mt0) REVERT: E 414 ASP cc_start: 0.6886 (p0) cc_final: 0.6638 (p0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0852 time to fit residues: 21.2524 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.0000 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163959 restraints weight = 15086.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.168114 restraints weight = 9104.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170942 restraints weight = 6268.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.172917 restraints weight = 4720.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.174003 restraints weight = 3795.572| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8787 Z= 0.136 Angle : 0.720 9.705 11960 Z= 0.323 Chirality : 0.044 0.271 1384 Planarity : 0.005 0.046 1497 Dihedral : 7.908 78.200 1549 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.24), residues: 1017 helix: 0.14 (0.44), residues: 133 sheet: -1.55 (0.43), residues: 161 loop : -2.60 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 153 TYR 0.023 0.002 TYR B 74 PHE 0.017 0.001 PHE A 228 TRP 0.011 0.001 TRP A 279 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8754) covalent geometry : angle 0.70126 (11874) SS BOND : bond 0.00258 ( 13) SS BOND : angle 1.02135 ( 26) hydrogen bonds : bond 0.03163 ( 130) hydrogen bonds : angle 4.64221 ( 351) link_BETA1-3 : bond 0.00502 ( 1) link_BETA1-3 : angle 4.17136 ( 3) link_BETA1-4 : bond 0.00451 ( 11) link_BETA1-4 : angle 1.83460 ( 33) link_NAG-ASN : bond 0.00293 ( 8) link_NAG-ASN : angle 2.65580 ( 24) *********************** 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 179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8123 (ptt90) REVERT: A 151 ARG cc_start: 0.7840 (ptp90) cc_final: 0.7621 (ptp90) REVERT: A 152 TYR cc_start: 0.7116 (t80) cc_final: 0.6776 (t80) REVERT: A 171 VAL cc_start: 0.7985 (m) cc_final: 0.7363 (t) REVERT: A 333 GLU cc_start: 0.7328 (pt0) cc_final: 0.7051 (pt0) REVERT: A 338 VAL cc_start: 0.7987 (t) cc_final: 0.7651 (p) REVERT: A 346 LYS cc_start: 0.8412 (pttm) cc_final: 0.8198 (pttp) REVERT: B 301 TRP cc_start: 0.7553 (m100) cc_final: 0.7343 (m100) REVERT: B 349 GLN cc_start: 0.7330 (tt0) cc_final: 0.7051 (tt0) REVERT: E 146 LEU cc_start: 0.8417 (mt) cc_final: 0.8190 (mt) REVERT: E 315 LEU cc_start: 0.7994 (tp) cc_final: 0.7683 (tp) REVERT: E 319 GLN cc_start: 0.8029 (mp10) cc_final: 0.7155 (mp10) REVERT: E 343 GLN cc_start: 0.7422 (mt0) cc_final: 0.7081 (mt0) REVERT: E 389 PHE cc_start: 0.7396 (t80) cc_final: 0.6905 (t80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0994 time to fit residues: 23.6430 Evaluate side-chains 165 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165402 restraints weight = 15395.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.169675 restraints weight = 9182.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.172512 restraints weight = 6272.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.174503 restraints weight = 4720.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175589 restraints weight = 3793.765| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4119 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= 0.104 Angle : 0.691 10.082 11960 Z= 0.305 Chirality : 0.042 0.251 1384 Planarity : 0.004 0.041 1497 Dihedral : 7.348 74.862 1549 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.19 % Favored : 93.71 % Rotamer: Outliers : 0.11 % Allowed : 1.62 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.24), residues: 1017 helix: 0.48 (0.46), residues: 127 sheet: -1.46 (0.44), residues: 156 loop : -2.59 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 153 TYR 0.024 0.001 TYR B 74 PHE 0.015 0.001 PHE A 228 TRP 0.011 0.001 TRP B 279 HIS 0.009 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8754) covalent geometry : angle 0.67500 (11874) SS BOND : bond 0.00250 ( 13) SS BOND : angle 1.19846 ( 26) hydrogen bonds : bond 0.02677 ( 130) hydrogen bonds : angle 4.46140 ( 351) link_BETA1-3 : bond 0.00611 ( 1) link_BETA1-3 : angle 4.26703 ( 3) link_BETA1-4 : bond 0.00451 ( 11) link_BETA1-4 : angle 1.70212 ( 33) link_NAG-ASN : bond 0.00497 ( 8) link_NAG-ASN : angle 2.21011 ( 24) *********************** 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 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8111 (ptt90) REVERT: A 104 MET cc_start: 0.6342 (mmm) cc_final: 0.6123 (mmt) REVERT: A 151 ARG cc_start: 0.7898 (ptp90) cc_final: 0.7584 (ptp90) REVERT: A 152 TYR cc_start: 0.7015 (t80) cc_final: 0.6725 (t80) REVERT: A 171 VAL cc_start: 0.7919 (m) cc_final: 0.7294 (t) REVERT: A 232 MET cc_start: 0.7043 (mtm) cc_final: 0.6828 (mtm) REVERT: A 333 GLU cc_start: 0.7339 (pt0) cc_final: 0.7101 (pt0) REVERT: A 338 VAL cc_start: 0.7908 (t) cc_final: 0.7548 (p) REVERT: B 349 GLN cc_start: 0.7377 (tt0) cc_final: 0.7119 (tt0) REVERT: E 130 MET cc_start: 0.3627 (mmp) cc_final: 0.3343 (mmm) REVERT: E 146 LEU cc_start: 0.8320 (mt) cc_final: 0.8115 (mt) REVERT: E 315 LEU cc_start: 0.8155 (tp) cc_final: 0.7796 (tt) REVERT: E 319 GLN cc_start: 0.8045 (mp10) cc_final: 0.7122 (mp10) REVERT: E 343 GLN cc_start: 0.7509 (mt0) cc_final: 0.7203 (mt0) REVERT: E 389 PHE cc_start: 0.7342 (t80) cc_final: 0.6877 (t80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1022 time to fit residues: 25.2007 Evaluate side-chains 167 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN E 88 HIS E 102 ASN E 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158969 restraints weight = 14861.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162976 restraints weight = 9036.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165730 restraints weight = 6242.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.167576 restraints weight = 4718.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.168998 restraints weight = 3819.067| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8787 Z= 0.186 Angle : 0.800 11.509 11960 Z= 0.365 Chirality : 0.047 0.285 1384 Planarity : 0.006 0.060 1497 Dihedral : 7.734 71.711 1549 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.55 % Favored : 91.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.24), residues: 1017 helix: 0.30 (0.46), residues: 122 sheet: -1.74 (0.39), residues: 186 loop : -2.56 (0.20), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 81 TYR 0.023 0.002 TYR B 270 PHE 0.015 0.002 PHE E 389 TRP 0.023 0.002 TRP B 301 HIS 0.008 0.002 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8754) covalent geometry : angle 0.78170 (11874) SS BOND : bond 0.00577 ( 13) SS BOND : angle 1.62477 ( 26) hydrogen bonds : bond 0.03552 ( 130) hydrogen bonds : angle 4.73245 ( 351) link_BETA1-3 : bond 0.00259 ( 1) link_BETA1-3 : angle 4.62444 ( 3) link_BETA1-4 : bond 0.00426 ( 11) link_BETA1-4 : angle 1.98409 ( 33) link_NAG-ASN : bond 0.00363 ( 8) link_NAG-ASN : angle 2.35191 ( 24) *********************** 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 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7217 (t80) cc_final: 0.6988 (t80) REVERT: A 81 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8213 (ptt90) REVERT: A 152 TYR cc_start: 0.7227 (t80) cc_final: 0.6851 (t80) REVERT: A 171 VAL cc_start: 0.8066 (m) cc_final: 0.7506 (t) REVERT: A 269 LEU cc_start: 0.8472 (tt) cc_final: 0.8060 (tt) REVERT: A 327 CYS cc_start: 0.4713 (t) cc_final: 0.4478 (t) REVERT: A 333 GLU cc_start: 0.7668 (pt0) cc_final: 0.7229 (pt0) REVERT: A 339 TYR cc_start: 0.7568 (p90) cc_final: 0.7356 (p90) REVERT: B 292 PHE cc_start: 0.7024 (p90) cc_final: 0.6665 (p90) REVERT: B 348 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6841 (tt0) REVERT: B 349 GLN cc_start: 0.7416 (tt0) cc_final: 0.7179 (tt0) REVERT: E 257 ARG cc_start: 0.7343 (ptm160) cc_final: 0.7107 (ptm-80) REVERT: E 315 LEU cc_start: 0.8031 (tp) cc_final: 0.7685 (tt) REVERT: E 317 MET cc_start: 0.7047 (mtm) cc_final: 0.6097 (mtm) REVERT: E 318 SER cc_start: 0.7582 (p) cc_final: 0.6208 (p) REVERT: E 319 GLN cc_start: 0.7852 (mp10) cc_final: 0.7105 (mp10) REVERT: E 414 ASP cc_start: 0.7166 (p0) cc_final: 0.6812 (p0) REVERT: E 443 MET cc_start: 0.6535 (ppp) cc_final: 0.6145 (ptt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1003 time to fit residues: 25.4167 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 : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 316 GLN E 102 ASN E 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158644 restraints weight = 14823.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162676 restraints weight = 9012.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165473 restraints weight = 6230.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167305 restraints weight = 4678.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168751 restraints weight = 3773.958| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8787 Z= 0.145 Angle : 0.763 12.654 11960 Z= 0.344 Chirality : 0.045 0.261 1384 Planarity : 0.005 0.077 1497 Dihedral : 7.464 68.211 1549 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.24), residues: 1017 helix: 0.39 (0.46), residues: 122 sheet: -1.53 (0.38), residues: 189 loop : -2.59 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 151 TYR 0.015 0.002 TYR A 52 PHE 0.015 0.002 PHE E 389 TRP 0.019 0.002 TRP B 301 HIS 0.007 0.001 HIS E 342 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8754) covalent geometry : angle 0.74604 (11874) SS BOND : bond 0.00198 ( 13) SS BOND : angle 1.41216 ( 26) hydrogen bonds : bond 0.03219 ( 130) hydrogen bonds : angle 4.54953 ( 351) link_BETA1-3 : bond 0.00513 ( 1) link_BETA1-3 : angle 4.60782 ( 3) link_BETA1-4 : bond 0.00441 ( 11) link_BETA1-4 : angle 1.81368 ( 33) link_NAG-ASN : bond 0.00328 ( 8) link_NAG-ASN : angle 2.26141 ( 24) *********************** 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 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8182 (ptt90) REVERT: A 171 VAL cc_start: 0.8122 (m) cc_final: 0.7508 (t) REVERT: A 269 LEU cc_start: 0.8408 (tt) cc_final: 0.8007 (tt) REVERT: A 333 GLU cc_start: 0.7701 (pt0) cc_final: 0.7217 (pt0) REVERT: A 338 VAL cc_start: 0.8185 (t) cc_final: 0.7876 (p) REVERT: B 18 GLU cc_start: 0.7798 (tp30) cc_final: 0.7142 (tp30) REVERT: B 84 MET cc_start: 0.6951 (ptp) cc_final: 0.6571 (ptt) REVERT: B 348 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6715 (tt0) REVERT: B 349 GLN cc_start: 0.7355 (tt0) cc_final: 0.7037 (tt0) REVERT: B 352 ASN cc_start: 0.8309 (m-40) cc_final: 0.8007 (m-40) REVERT: E 146 LEU cc_start: 0.8360 (mt) cc_final: 0.8068 (mt) REVERT: E 257 ARG cc_start: 0.7397 (ptm160) cc_final: 0.7156 (ptm-80) REVERT: E 315 LEU cc_start: 0.8038 (tp) cc_final: 0.7804 (tp) REVERT: E 317 MET cc_start: 0.7091 (mtm) cc_final: 0.6418 (mtm) REVERT: E 318 SER cc_start: 0.7571 (p) cc_final: 0.6829 (p) REVERT: E 443 MET cc_start: 0.6616 (ppp) cc_final: 0.6213 (ptt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0972 time to fit residues: 26.4955 Evaluate side-chains 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 283 HIS E 102 ASN E 320 ASN ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159785 restraints weight = 14934.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164052 restraints weight = 8856.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167011 restraints weight = 6020.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168924 restraints weight = 4469.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170454 restraints weight = 3578.535| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8787 Z= 0.121 Angle : 0.747 12.699 11960 Z= 0.333 Chirality : 0.044 0.259 1384 Planarity : 0.005 0.069 1497 Dihedral : 7.118 64.012 1549 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.15 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.24), residues: 1017 helix: 0.43 (0.45), residues: 122 sheet: -1.44 (0.40), residues: 166 loop : -2.65 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 151 TYR 0.017 0.001 TYR A 340 PHE 0.015 0.001 PHE B 188 TRP 0.017 0.001 TRP B 301 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8754) covalent geometry : angle 0.73131 (11874) SS BOND : bond 0.00188 ( 13) SS BOND : angle 1.24766 ( 26) hydrogen bonds : bond 0.03036 ( 130) hydrogen bonds : angle 4.45190 ( 351) link_BETA1-3 : bond 0.00562 ( 1) link_BETA1-3 : angle 4.71252 ( 3) link_BETA1-4 : bond 0.00427 ( 11) link_BETA1-4 : angle 1.73600 ( 33) link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 2.13151 ( 24) ********************** 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: 1 poor density : 201 time to evaluate : 0.351 Fit side-chains REVERT: A 52 TYR cc_start: 0.7201 (t80) cc_final: 0.6997 (t80) REVERT: A 81 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8202 (ptt90) REVERT: A 104 MET cc_start: 0.5013 (mmt) cc_final: 0.4673 (mmm) REVERT: A 154 SER cc_start: 0.6979 (p) cc_final: 0.6433 (m) REVERT: A 171 VAL cc_start: 0.8036 (m) cc_final: 0.7455 (t) REVERT: A 269 LEU cc_start: 0.8401 (tt) cc_final: 0.7988 (tt) REVERT: A 289 HIS cc_start: 0.6910 (m-70) cc_final: 0.6700 (m-70) REVERT: A 333 GLU cc_start: 0.7722 (pt0) cc_final: 0.7207 (pt0) REVERT: B 18 GLU cc_start: 0.7861 (tp30) cc_final: 0.7155 (tp30) REVERT: B 84 MET cc_start: 0.7035 (ptp) cc_final: 0.6611 (ptt) REVERT: B 292 PHE cc_start: 0.6987 (p90) cc_final: 0.6642 (p90) REVERT: B 348 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6757 (tt0) REVERT: E 146 LEU cc_start: 0.8312 (mt) cc_final: 0.8091 (mt) REVERT: E 149 ASN cc_start: 0.8054 (m-40) cc_final: 0.7515 (m-40) REVERT: E 257 ARG cc_start: 0.7435 (ptm160) cc_final: 0.7120 (ptm-80) REVERT: E 315 LEU cc_start: 0.7943 (tp) cc_final: 0.7630 (tt) REVERT: E 319 GLN cc_start: 0.8130 (mp10) cc_final: 0.7469 (mp10) REVERT: E 343 GLN cc_start: 0.7648 (mt0) cc_final: 0.7336 (mt0) REVERT: E 366 SER cc_start: 0.7784 (p) cc_final: 0.7505 (p) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.0888 time to fit residues: 24.4161 Evaluate side-chains 188 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.178999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158767 restraints weight = 14661.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162824 restraints weight = 8850.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165599 restraints weight = 6051.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167555 restraints weight = 4517.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168595 restraints weight = 3594.219| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8787 Z= 0.142 Angle : 0.771 12.006 11960 Z= 0.346 Chirality : 0.044 0.244 1384 Planarity : 0.005 0.066 1497 Dihedral : 7.046 60.562 1549 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.36 % Favored : 91.54 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.24), residues: 1017 helix: 0.50 (0.45), residues: 122 sheet: -1.61 (0.39), residues: 180 loop : -2.66 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 118 TYR 0.019 0.002 TYR A 340 PHE 0.011 0.001 PHE B 95 TRP 0.023 0.002 TRP A 178 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8754) covalent geometry : angle 0.75580 (11874) SS BOND : bond 0.00204 ( 13) SS BOND : angle 1.24621 ( 26) hydrogen bonds : bond 0.03248 ( 130) hydrogen bonds : angle 4.57723 ( 351) link_BETA1-3 : bond 0.00407 ( 1) link_BETA1-3 : angle 4.82776 ( 3) link_BETA1-4 : bond 0.00448 ( 11) link_BETA1-4 : angle 1.79200 ( 33) link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 2.14181 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.11 seconds wall clock time: 24 minutes 30.27 seconds (1470.27 seconds total)