Starting phenix.real_space_refine on Thu Jul 2 12:20:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1r_33571/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1r_33571/07_2026/7y1r_33571.map" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.49, per 1000 atoms: 0.17 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: 0.49 Conformation dependent library (CDL) restraints added in 324.0 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: 0.23 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: 1.05 Time building geometry restraints manager: 0.69 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 - 17.92: 4727 17.92 - 35.83: 393 35.83 - 53.75: 72 53.75 - 71.66: 6 71.66 - 89.58: 9 Dihedral angle restraints: 5207 sinusoidal: 2152 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 5204 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: 1.120 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 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 : 13.081 89.580 3182 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/Z covalent geometry : bond 0.00330 / 0.16 ( 8754) covalent geometry : angle 0.70418 / 0.30 (11874) SS BOND : bond 0.00129 / 0.07 ( 13) SS BOND : angle 0.77790 / 0.45 ( 26) hydrogen bonds : bond 0.22318 / 16.05 ( 130) hydrogen bonds : angle 7.91424 / 6.04 ( 351) link_BETA1-3 : bond 0.01056 / 0.56 ( 1) link_BETA1-3 : angle 1.71039 / 0.90 ( 3) link_BETA1-4 : bond 0.00397 / 0.24 ( 11) link_BETA1-4 : angle 1.37530 / 0.79 ( 33) link_NAG-ASN : bond 0.00182 / 0.08 ( 8) link_NAG-ASN : angle 1.84553 / 0.92 ( 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 : 0.333 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: 0.1006 time to fit residues: 22.7670 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: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4463 r_free = 0.4463 target = 0.197395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.176399 restraints weight = 15474.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180511 restraints weight = 9479.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.183399 restraints weight = 6596.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.185421 restraints weight = 5003.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.186682 restraints weight = 4028.227| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.1693 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= 0.150 Angle : 0.694 9.151 11960 Z= 0.320 Chirality : 0.044 0.289 1384 Planarity : 0.005 0.081 1497 Dihedral : 3.753 16.181 1139 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: -2.85 (0.24), residues: 1017 helix: 0.05 (0.45), residues: 128 sheet: -1.56 (0.45), residues: 143 loop : -2.53 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 153 TYR 0.014 0.002 TYR A 152 PHE 0.014 0.002 PHE E 389 TRP 0.016 0.002 TRP A 281 HIS 0.009 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8754) covalent geometry : angle 0.67862 / 0.32 (11874) SS BOND : bond 0.00268 / 0.19 ( 13) SS BOND : angle 1.06055 / 0.61 ( 26) hydrogen bonds : bond 0.03410 / 2.26 ( 130) hydrogen bonds : angle 5.17267 / 4.10 ( 351) link_BETA1-3 : bond 0.00929 / 0.49 ( 1) link_BETA1-3 : angle 2.62247 / 1.01 ( 3) link_BETA1-4 : bond 0.00491 / 0.31 ( 11) link_BETA1-4 : angle 2.12726 / 1.21 ( 33) link_NAG-ASN : bond 0.00393 / 0.20 ( 8) link_NAG-ASN : angle 2.01586 / 1.15 ( 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 176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7881 (tp40) cc_final: 0.7527 (tp-100) REVERT: A 77 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7791 (mtpp) REVERT: A 84 MET cc_start: 0.4865 (tpt) cc_final: 0.4470 (tpt) REVERT: A 111 LEU cc_start: 0.6827 (mm) cc_final: 0.6585 (mt) REVERT: A 151 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6701 (ptp90) REVERT: A 279 TRP cc_start: 0.7966 (p90) cc_final: 0.7612 (p90) REVERT: A 346 LYS cc_start: 0.8377 (pttm) cc_final: 0.7966 (pttm) REVERT: B 15 LYS cc_start: 0.8362 (tppt) cc_final: 0.7770 (tppt) REVERT: B 74 TYR cc_start: 0.6565 (t80) cc_final: 0.6309 (t80) REVERT: B 353 MET cc_start: 0.8066 (mmp) cc_final: 0.7660 (mmp) REVERT: E 264 ASN cc_start: 0.6924 (m-40) cc_final: 0.6717 (m-40) REVERT: E 319 GLN cc_start: 0.7918 (mp10) cc_final: 0.7669 (mp10) REVERT: E 414 ASP cc_start: 0.6226 (p0) cc_final: 0.5942 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0943 time to fit residues: 22.6120 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 : 0.300 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 0.0030 chunk 24 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.0030 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.197640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.177591 restraints weight = 15312.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181405 restraints weight = 9729.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.184085 restraints weight = 6919.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185913 restraints weight = 5335.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.187127 restraints weight = 4358.537| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.1984 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= 0.109 Angle : 0.622 9.388 11960 Z= 0.280 Chirality : 0.041 0.247 1384 Planarity : 0.004 0.065 1497 Dihedral : 3.574 16.177 1139 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.44), residues: 134 sheet: -1.65 (0.43), residues: 159 loop : -2.49 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 153 TYR 0.019 0.001 TYR B 314 PHE 0.010 0.001 PHE B 228 TRP 0.024 0.002 TRP A 281 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 8754) covalent geometry : angle 0.60941 / 0.28 (11874) SS BOND : bond 0.00159 / 0.09 ( 13) SS BOND : angle 0.95825 / 0.55 ( 26) hydrogen bonds : bond 0.03340 / 2.27 ( 130) hydrogen bonds : angle 4.93621 / 3.95 ( 351) link_BETA1-3 : bond 0.01098 / 0.58 ( 1) link_BETA1-3 : angle 2.09265 / 0.97 ( 3) link_BETA1-4 : bond 0.00456 / 0.28 ( 11) link_BETA1-4 : angle 1.52998 / 0.89 ( 33) link_NAG-ASN : bond 0.00276 / 0.17 ( 8) link_NAG-ASN : angle 2.01313 / 1.12 ( 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 173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.4795 (tpt) cc_final: 0.4451 (tpt) REVERT: A 151 ARG cc_start: 0.7140 (ptp90) cc_final: 0.6685 (ptp90) REVERT: A 171 VAL cc_start: 0.7766 (m) cc_final: 0.7102 (t) REVERT: A 289 HIS cc_start: 0.6388 (m-70) cc_final: 0.6037 (m-70) REVERT: A 333 GLU cc_start: 0.6337 (pt0) cc_final: 0.6117 (pt0) REVERT: B 18 GLU cc_start: 0.7756 (tp30) cc_final: 0.7511 (tp30) REVERT: B 74 TYR cc_start: 0.6671 (t80) cc_final: 0.6442 (t80) REVERT: B 301 TRP cc_start: 0.7221 (m100) cc_final: 0.6743 (m100) REVERT: B 333 GLU cc_start: 0.7073 (mp0) cc_final: 0.6798 (mp0) REVERT: E 317 MET cc_start: 0.6704 (mtp) cc_final: 0.6366 (mtp) REVERT: E 319 GLN cc_start: 0.7897 (mp10) cc_final: 0.7632 (mp10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1032 time to fit residues: 24.1134 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 : 0.319 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 0.0370 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.191886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.171059 restraints weight = 15710.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175051 restraints weight = 9589.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.177809 restraints weight = 6685.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.179801 restraints weight = 5074.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181046 restraints weight = 4087.480| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.2717 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= 0.121 Angle : 0.655 9.680 11960 Z= 0.293 Chirality : 0.042 0.279 1384 Planarity : 0.004 0.055 1497 Dihedral : 3.662 15.747 1139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -2.75 (0.24), residues: 1017 helix: 0.15 (0.44), residues: 134 sheet: -1.58 (0.44), residues: 160 loop : -2.46 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 153 TYR 0.023 0.001 TYR B 314 PHE 0.010 0.001 PHE E 314 TRP 0.031 0.002 TRP A 281 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8754) covalent geometry : angle 0.64404 / 0.29 (11874) SS BOND : bond 0.00211 / 0.12 ( 13) SS BOND : angle 0.83567 / 0.49 ( 26) hydrogen bonds : bond 0.02959 / 1.96 ( 130) hydrogen bonds : angle 4.62286 / 3.63 ( 351) link_BETA1-3 : bond 0.00998 / 0.53 ( 1) link_BETA1-3 : angle 2.21549 / 0.98 ( 3) link_BETA1-4 : bond 0.00384 / 0.24 ( 11) link_BETA1-4 : angle 1.54994 / 0.89 ( 33) link_NAG-ASN : bond 0.00221 / 0.14 ( 8) link_NAG-ASN : angle 1.92086 / 1.01 ( 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 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.4713 (tpt) cc_final: 0.4371 (tpt) REVERT: A 151 ARG cc_start: 0.7627 (ptp90) cc_final: 0.7277 (ptp90) REVERT: A 152 TYR cc_start: 0.6833 (t80) cc_final: 0.6472 (t80) REVERT: A 171 VAL cc_start: 0.7898 (m) cc_final: 0.7260 (t) REVERT: A 269 LEU cc_start: 0.7703 (tt) cc_final: 0.7405 (tt) REVERT: A 289 HIS cc_start: 0.6686 (m-70) cc_final: 0.6173 (m-70) REVERT: A 338 VAL cc_start: 0.7603 (t) cc_final: 0.7239 (p) REVERT: B 74 TYR cc_start: 0.6845 (t80) cc_final: 0.6563 (t80) REVERT: B 299 TYR cc_start: 0.6920 (t80) cc_final: 0.6673 (t80) REVERT: B 301 TRP cc_start: 0.7370 (m100) cc_final: 0.7068 (m100) REVERT: E 90 ARG cc_start: 0.6792 (tpp-160) cc_final: 0.6536 (tpp-160) REVERT: E 317 MET cc_start: 0.6856 (mtp) cc_final: 0.6259 (mtp) REVERT: E 319 GLN cc_start: 0.7918 (mp10) cc_final: 0.7530 (mp10) REVERT: E 415 MET cc_start: 0.6137 (pmm) cc_final: 0.5921 (pmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0951 time to fit residues: 23.5720 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 : 0.298 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 342 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.175720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155279 restraints weight = 15012.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159201 restraints weight = 9183.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161911 restraints weight = 6392.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163834 restraints weight = 4846.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165038 restraints weight = 3900.270| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8787 Z= 0.290 Angle : 0.993 11.856 11960 Z= 0.469 Chirality : 0.055 0.337 1384 Planarity : 0.007 0.063 1497 Dihedral : 5.647 22.635 1139 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.32 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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: -3.25 (0.23), residues: 1017 helix: -0.46 (0.44), residues: 126 sheet: -1.70 (0.39), residues: 175 loop : -2.81 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 190 TYR 0.034 0.003 TYR E 471 PHE 0.034 0.003 PHE E 389 TRP 0.041 0.004 TRP A 279 HIS 0.011 0.003 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.29 ( 8754) covalent geometry : angle 0.97460 / 0.46 (11874) SS BOND : bond 0.00906 / 0.62 ( 13) SS BOND : angle 1.47903 / 0.94 ( 26) hydrogen bonds : bond 0.04640 / 3.04 ( 130) hydrogen bonds : angle 5.09671 / 3.80 ( 351) link_BETA1-3 : bond 0.00582 / 0.31 ( 1) link_BETA1-3 : angle 2.85006 / 1.06 ( 3) link_BETA1-4 : bond 0.00535 / 0.34 ( 11) link_BETA1-4 : angle 2.31278 / 1.34 ( 33) link_NAG-ASN : bond 0.00597 / 0.30 ( 8) link_NAG-ASN : angle 3.27691 / 1.67 ( 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 207 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.308 Fit side-chains REVERT: A 29 ARG cc_start: 0.7419 (tmm160) cc_final: 0.7134 (tmm160) REVERT: A 79 VAL cc_start: 0.8181 (p) cc_final: 0.7879 (t) REVERT: A 81 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8258 (ptt90) REVERT: A 152 TYR cc_start: 0.7253 (t80) cc_final: 0.6843 (t80) REVERT: A 171 VAL cc_start: 0.8220 (m) cc_final: 0.7739 (t) REVERT: A 232 MET cc_start: 0.7174 (mtm) cc_final: 0.6787 (mtm) REVERT: A 289 HIS cc_start: 0.6974 (m-70) cc_final: 0.6529 (m-70) REVERT: A 333 GLU cc_start: 0.7802 (pt0) cc_final: 0.7353 (pt0) REVERT: A 346 LYS cc_start: 0.8443 (pttp) cc_final: 0.8075 (pttp) REVERT: B 18 GLU cc_start: 0.7771 (tp30) cc_final: 0.7050 (tp30) REVERT: B 24 ILE cc_start: 0.7720 (mm) cc_final: 0.7213 (mt) REVERT: B 74 TYR cc_start: 0.7761 (t80) cc_final: 0.7479 (t80) REVERT: B 175 VAL cc_start: 0.7771 (t) cc_final: 0.7526 (p) REVERT: B 176 ARG cc_start: 0.7415 (tpp80) cc_final: 0.7206 (tpp80) REVERT: B 232 MET cc_start: 0.6592 (mmm) cc_final: 0.6354 (mtt) REVERT: B 283 HIS cc_start: 0.7560 (m90) cc_final: 0.7101 (m-70) REVERT: B 355 VAL cc_start: 0.8217 (p) cc_final: 0.7942 (m) REVERT: E 92 LEU cc_start: 0.7178 (tp) cc_final: 0.6842 (tp) REVERT: E 149 ASN cc_start: 0.7936 (m-40) cc_final: 0.7450 (m-40) REVERT: E 173 ASN cc_start: 0.7771 (m-40) cc_final: 0.7358 (m-40) REVERT: E 215 VAL cc_start: 0.8672 (t) cc_final: 0.8174 (p) REVERT: E 233 GLU cc_start: 0.6763 (pp20) cc_final: 0.6478 (pp20) REVERT: E 257 ARG cc_start: 0.7403 (ptm160) cc_final: 0.7137 (ptm-80) REVERT: E 318 SER cc_start: 0.7889 (p) cc_final: 0.6553 (p) REVERT: E 319 GLN cc_start: 0.7642 (mp10) cc_final: 0.6738 (mp10) REVERT: E 333 MET cc_start: 0.6138 (mmm) cc_final: 0.5660 (mmm) REVERT: E 414 ASP cc_start: 0.7292 (p0) cc_final: 0.7029 (p0) REVERT: E 443 MET cc_start: 0.6586 (ppp) cc_final: 0.6187 (ptt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1056 time to fit residues: 29.2347 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 0.6980 chunk 7 optimal weight: 0.0060 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 16 optimal weight: 0.0070 chunk 64 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN E 102 ASN E 320 ASN ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.182484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161628 restraints weight = 14946.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165821 restraints weight = 9006.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.168676 restraints weight = 6186.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170656 restraints weight = 4665.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.172072 restraints weight = 3738.639| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8787 Z= 0.121 Angle : 0.763 14.034 11960 Z= 0.341 Chirality : 0.045 0.261 1384 Planarity : 0.005 0.112 1497 Dihedral : 4.660 21.777 1139 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.98 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.96 (0.24), residues: 1017 helix: 0.14 (0.45), residues: 127 sheet: -1.65 (0.39), residues: 180 loop : -2.65 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 117 TYR 0.016 0.001 TYR E 174 PHE 0.010 0.001 PHE B 228 TRP 0.010 0.001 TRP A 279 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8754) covalent geometry : angle 0.74471 / 0.34 (11874) SS BOND : bond 0.00272 / 0.18 ( 13) SS BOND : angle 1.80411 / 1.10 ( 26) hydrogen bonds : bond 0.03025 / 1.99 ( 130) hydrogen bonds : angle 4.75427 / 3.66 ( 351) link_BETA1-3 : bond 0.01053 / 0.55 ( 1) link_BETA1-3 : angle 2.17202 / 1.03 ( 3) link_BETA1-4 : bond 0.00449 / 0.28 ( 11) link_BETA1-4 : angle 1.54530 / 0.89 ( 33) link_NAG-ASN : bond 0.00400 / 0.24 ( 8) link_NAG-ASN : angle 2.91728 / 1.63 ( 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 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8235 (ptt90) REVERT: A 130 ARG cc_start: 0.4272 (tmm160) cc_final: 0.3969 (tmm160) REVERT: A 171 VAL cc_start: 0.8021 (m) cc_final: 0.7550 (t) REVERT: A 228 PHE cc_start: 0.7510 (p90) cc_final: 0.7310 (p90) REVERT: A 333 GLU cc_start: 0.7617 (pt0) cc_final: 0.7223 (pt0) REVERT: B 18 GLU cc_start: 0.7558 (tp30) cc_final: 0.6941 (tp30) REVERT: B 176 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6950 (tpp80) REVERT: B 228 PHE cc_start: 0.5813 (m-10) cc_final: 0.4708 (m-10) REVERT: B 355 VAL cc_start: 0.7966 (p) cc_final: 0.7709 (m) REVERT: B 359 LYS cc_start: 0.7583 (ptpp) cc_final: 0.7378 (ptpp) REVERT: E 76 GLU cc_start: 0.6575 (tt0) cc_final: 0.6306 (tt0) REVERT: E 315 LEU cc_start: 0.8163 (tp) cc_final: 0.7685 (tt) REVERT: E 317 MET cc_start: 0.6773 (mtp) cc_final: 0.6312 (mtm) REVERT: E 318 SER cc_start: 0.7713 (p) cc_final: 0.6314 (p) REVERT: E 319 GLN cc_start: 0.7908 (mp10) cc_final: 0.7126 (mp10) REVERT: E 343 GLN cc_start: 0.7710 (mt0) cc_final: 0.7447 (mt0) REVERT: E 414 ASP cc_start: 0.7192 (p0) cc_final: 0.6904 (p0) REVERT: E 443 MET cc_start: 0.6345 (ppp) cc_final: 0.5787 (ptt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1099 time to fit residues: 27.6063 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 320 ASN E 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.181568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160586 restraints weight = 15194.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164724 restraints weight = 9107.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.167613 restraints weight = 6298.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169582 restraints weight = 4733.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.170970 restraints weight = 3813.328| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4944 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= 0.116 Angle : 0.718 13.630 11960 Z= 0.323 Chirality : 0.044 0.265 1384 Planarity : 0.006 0.114 1497 Dihedral : 4.560 23.817 1139 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 0.23 (0.46), residues: 127 sheet: -1.55 (0.40), residues: 167 loop : -2.61 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 81 TYR 0.016 0.001 TYR A 340 PHE 0.008 0.001 PHE B 95 TRP 0.017 0.001 TRP A 178 HIS 0.007 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8754) covalent geometry : angle 0.70108 / 0.32 (11874) SS BOND : bond 0.00174 / 0.11 ( 13) SS BOND : angle 1.63103 / 1.00 ( 26) hydrogen bonds : bond 0.03068 / 2.02 ( 130) hydrogen bonds : angle 4.73374 / 3.58 ( 351) link_BETA1-3 : bond 0.00918 / 0.48 ( 1) link_BETA1-3 : angle 2.29229 / 1.07 ( 3) link_BETA1-4 : bond 0.00412 / 0.26 ( 11) link_BETA1-4 : angle 1.57357 / 0.92 ( 33) link_NAG-ASN : bond 0.00380 / 0.21 ( 8) link_NAG-ASN : angle 2.59315 / 1.42 ( 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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7204 (t80) cc_final: 0.6770 (t80) REVERT: A 81 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8184 (ptt90) REVERT: A 104 MET cc_start: 0.5704 (mmt) cc_final: 0.5341 (mmm) REVERT: A 130 ARG cc_start: 0.4540 (tmm160) cc_final: 0.4247 (tmm160) REVERT: A 171 VAL cc_start: 0.7922 (m) cc_final: 0.7415 (t) REVERT: A 228 PHE cc_start: 0.7518 (p90) cc_final: 0.7283 (p90) REVERT: A 333 GLU cc_start: 0.7733 (pt0) cc_final: 0.7299 (pt0) REVERT: B 18 GLU cc_start: 0.7679 (tp30) cc_final: 0.7062 (tp30) REVERT: B 355 VAL cc_start: 0.7963 (p) cc_final: 0.7727 (m) REVERT: E 76 GLU cc_start: 0.6593 (tt0) cc_final: 0.6305 (tt0) REVERT: E 146 LEU cc_start: 0.8315 (mt) cc_final: 0.8104 (mt) REVERT: E 315 LEU cc_start: 0.8213 (tp) cc_final: 0.7660 (tt) REVERT: E 318 SER cc_start: 0.7557 (p) cc_final: 0.6278 (p) REVERT: E 319 GLN cc_start: 0.7992 (mp10) cc_final: 0.7169 (mp10) REVERT: E 339 LEU cc_start: 0.8127 (tp) cc_final: 0.7904 (tt) REVERT: E 414 ASP cc_start: 0.7154 (p0) cc_final: 0.6795 (p0) REVERT: E 443 MET cc_start: 0.6440 (ppp) cc_final: 0.5942 (ptt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1093 time to fit residues: 27.2493 Evaluate side-chains 174 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.5980 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 102 ASN E 320 ASN E 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.160321 restraints weight = 14824.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164373 restraints weight = 8891.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167228 restraints weight = 6110.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.169154 restraints weight = 4582.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170648 restraints weight = 3683.685| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.5175 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= 0.129 Angle : 0.734 14.403 11960 Z= 0.332 Chirality : 0.044 0.271 1384 Planarity : 0.005 0.051 1497 Dihedral : 4.511 24.115 1139 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.85 (0.24), residues: 1017 helix: 0.28 (0.45), residues: 127 sheet: -1.43 (0.39), residues: 176 loop : -2.63 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 153 TYR 0.014 0.001 TYR E 174 PHE 0.012 0.001 PHE B 228 TRP 0.011 0.001 TRP A 279 HIS 0.007 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8754) covalent geometry : angle 0.72016 / 0.33 (11874) SS BOND : bond 0.00201 / 0.12 ( 13) SS BOND : angle 1.21418 / 0.74 ( 26) hydrogen bonds : bond 0.03194 / 2.09 ( 130) hydrogen bonds : angle 4.72183 / 3.57 ( 351) link_BETA1-3 : bond 0.00662 / 0.35 ( 1) link_BETA1-3 : angle 2.41629 / 1.10 ( 3) link_BETA1-4 : bond 0.00399 / 0.24 ( 11) link_BETA1-4 : angle 1.59675 / 0.94 ( 33) link_NAG-ASN : bond 0.00279 / 0.17 ( 8) link_NAG-ASN : angle 2.44694 / 1.30 ( 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 181 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8223 (ptt90) REVERT: A 104 MET cc_start: 0.5836 (mmt) cc_final: 0.5429 (mmm) REVERT: A 154 SER cc_start: 0.6871 (p) cc_final: 0.6305 (m) REVERT: A 171 VAL cc_start: 0.7969 (m) cc_final: 0.7460 (t) REVERT: A 232 MET cc_start: 0.7264 (mtm) cc_final: 0.7061 (mtm) REVERT: B 18 GLU cc_start: 0.7837 (tp30) cc_final: 0.7090 (tp30) REVERT: B 74 TYR cc_start: 0.7588 (t80) cc_final: 0.7039 (t80) REVERT: B 355 VAL cc_start: 0.8009 (p) cc_final: 0.7778 (m) REVERT: E 76 GLU cc_start: 0.6813 (tt0) cc_final: 0.6384 (tt0) REVERT: E 146 LEU cc_start: 0.8286 (mt) cc_final: 0.8044 (mt) REVERT: E 212 VAL cc_start: 0.8669 (p) cc_final: 0.8445 (t) REVERT: E 315 LEU cc_start: 0.8194 (tp) cc_final: 0.7968 (tp) REVERT: E 317 MET cc_start: 0.6830 (mtm) cc_final: 0.6214 (ptm) REVERT: E 318 SER cc_start: 0.7531 (p) cc_final: 0.6218 (p) REVERT: E 319 GLN cc_start: 0.7968 (mp10) cc_final: 0.7299 (mp10) REVERT: E 320 ASN cc_start: 0.7568 (m-40) cc_final: 0.7337 (m-40) REVERT: E 339 LEU cc_start: 0.8185 (tp) cc_final: 0.7934 (tt) REVERT: E 367 HIS cc_start: 0.8099 (m90) cc_final: 0.7867 (m-70) REVERT: E 443 MET cc_start: 0.6520 (ppp) cc_final: 0.6115 (ptt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1087 time to fit residues: 26.1595 Evaluate side-chains 174 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 102 ASN E 342 HIS E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160968 restraints weight = 14677.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165007 restraints weight = 8823.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167791 restraints weight = 6065.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169772 restraints weight = 4551.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.171060 restraints weight = 3637.680| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8787 Z= 0.126 Angle : 0.736 15.120 11960 Z= 0.331 Chirality : 0.044 0.272 1384 Planarity : 0.005 0.050 1497 Dihedral : 4.450 23.120 1139 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -2.82 (0.24), residues: 1017 helix: 0.29 (0.46), residues: 127 sheet: -1.33 (0.39), residues: 175 loop : -2.63 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 90 TYR 0.018 0.001 TYR B 270 PHE 0.011 0.001 PHE A 105 TRP 0.019 0.001 TRP B 301 HIS 0.007 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8754) covalent geometry : angle 0.72198 / 0.33 (11874) SS BOND : bond 0.00265 / 0.16 ( 13) SS BOND : angle 1.33566 / 0.79 ( 26) hydrogen bonds : bond 0.03194 / 2.11 ( 130) hydrogen bonds : angle 4.90098 / 3.54 ( 351) link_BETA1-3 : bond 0.00823 / 0.43 ( 1) link_BETA1-3 : angle 2.40225 / 1.09 ( 3) link_BETA1-4 : bond 0.00397 / 0.25 ( 11) link_BETA1-4 : angle 1.58336 / 0.93 ( 33) link_NAG-ASN : bond 0.00274 / 0.17 ( 8) link_NAG-ASN : angle 2.39216 / 1.25 ( 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 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8186 (ptt90) REVERT: A 104 MET cc_start: 0.5126 (mmt) cc_final: 0.4868 (mmm) REVERT: A 154 SER cc_start: 0.6836 (p) cc_final: 0.6352 (m) REVERT: A 171 VAL cc_start: 0.7994 (m) cc_final: 0.7481 (t) REVERT: A 333 GLU cc_start: 0.7830 (pt0) cc_final: 0.7472 (mt-10) REVERT: B 18 GLU cc_start: 0.7724 (tp30) cc_final: 0.7079 (tp30) REVERT: B 78 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6797 (tm-30) REVERT: E 76 GLU cc_start: 0.6765 (tt0) cc_final: 0.6257 (tt0) REVERT: E 90 ARG cc_start: 0.7146 (tpp-160) cc_final: 0.6539 (tpp-160) REVERT: E 146 LEU cc_start: 0.8229 (mt) cc_final: 0.7979 (mt) REVERT: E 212 VAL cc_start: 0.8708 (p) cc_final: 0.8489 (t) REVERT: E 315 LEU cc_start: 0.8176 (tp) cc_final: 0.7835 (tp) REVERT: E 318 SER cc_start: 0.7492 (p) cc_final: 0.6252 (p) REVERT: E 319 GLN cc_start: 0.7886 (mp10) cc_final: 0.6880 (mp10) REVERT: E 339 LEU cc_start: 0.8194 (tp) cc_final: 0.7974 (tt) REVERT: E 367 HIS cc_start: 0.8066 (m90) cc_final: 0.7851 (m-70) REVERT: E 414 ASP cc_start: 0.6993 (p0) cc_final: 0.6539 (p0) REVERT: E 415 MET cc_start: 0.6673 (pmm) cc_final: 0.6224 (pmm) REVERT: E 443 MET cc_start: 0.6500 (ppp) cc_final: 0.6120 (ptt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1047 time to fit residues: 26.2783 Evaluate side-chains 177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.0370 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 349 GLN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153895 restraints weight = 14597.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.157831 restraints weight = 8887.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160635 restraints weight = 6171.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162432 restraints weight = 4645.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163904 restraints weight = 3766.842| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8787 Z= 0.216 Angle : 0.861 17.273 11960 Z= 0.398 Chirality : 0.048 0.300 1384 Planarity : 0.006 0.054 1497 Dihedral : 5.134 25.822 1139 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.83 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -3.07 (0.24), residues: 1017 helix: -0.07 (0.44), residues: 128 sheet: -1.80 (0.37), residues: 192 loop : -2.68 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 117 TYR 0.028 0.002 TYR A 52 PHE 0.021 0.002 PHE B 292 TRP 0.046 0.003 TRP A 178 HIS 0.009 0.002 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 ( 8754) covalent geometry : angle 0.84438 / 0.39 (11874) SS BOND : bond 0.00342 / 0.20 ( 13) SS BOND : angle 1.52510 / 0.92 ( 26) hydrogen bonds : bond 0.04010 / 2.61 ( 130) hydrogen bonds : angle 5.01770 / 3.64 ( 351) link_BETA1-3 : bond 0.00523 / 0.28 ( 1) link_BETA1-3 : angle 2.80638 / 1.15 ( 3) link_BETA1-4 : bond 0.00380 / 0.25 ( 11) link_BETA1-4 : angle 1.92413 / 1.14 ( 33) link_NAG-ASN : bond 0.00394 / 0.19 ( 8) link_NAG-ASN : angle 2.82624 / 1.45 ( 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 221 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6683 (tp30) cc_final: 0.6307 (tp30) REVERT: A 81 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8245 (ptt90) REVERT: A 104 MET cc_start: 0.5627 (mmt) cc_final: 0.5257 (mmm) REVERT: A 154 SER cc_start: 0.7222 (p) cc_final: 0.6814 (m) REVERT: A 171 VAL cc_start: 0.8155 (m) cc_final: 0.7948 (t) REVERT: A 231 LEU cc_start: 0.8174 (mm) cc_final: 0.7946 (mp) REVERT: A 232 MET cc_start: 0.7371 (mtm) cc_final: 0.7102 (mtm) REVERT: A 339 TYR cc_start: 0.7700 (p90) cc_final: 0.7471 (p90) REVERT: B 18 GLU cc_start: 0.7808 (tp30) cc_final: 0.6975 (tp30) REVERT: B 24 ILE cc_start: 0.7878 (mm) cc_final: 0.7417 (mt) REVERT: B 175 VAL cc_start: 0.7799 (t) cc_final: 0.7499 (p) REVERT: E 76 GLU cc_start: 0.7042 (tt0) cc_final: 0.6514 (tt0) REVERT: E 146 LEU cc_start: 0.8195 (mt) cc_final: 0.7921 (mt) REVERT: E 215 VAL cc_start: 0.8548 (t) cc_final: 0.8015 (p) REVERT: E 233 GLU cc_start: 0.6929 (pp20) cc_final: 0.6699 (pp20) REVERT: E 257 ARG cc_start: 0.7499 (ptm160) cc_final: 0.7244 (ptm-80) REVERT: E 315 LEU cc_start: 0.8287 (tp) cc_final: 0.7975 (tp) REVERT: E 317 MET cc_start: 0.7178 (mtm) cc_final: 0.6636 (mtm) REVERT: E 319 GLN cc_start: 0.7687 (mp10) cc_final: 0.7327 (mp10) REVERT: E 415 MET cc_start: 0.6741 (pmm) cc_final: 0.6405 (pmm) REVERT: E 443 MET cc_start: 0.6713 (ppp) cc_final: 0.6492 (ptt) REVERT: E 494 MET cc_start: 0.6374 (mpp) cc_final: 0.5741 (mpp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1093 time to fit residues: 32.1364 Evaluate side-chains 204 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 40 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 67 optimal weight: 0.0040 chunk 80 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 overall best weight: 0.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 102 ASN E 320 ASN E 342 HIS ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160051 restraints weight = 14587.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.164067 restraints weight = 8646.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166943 restraints weight = 5895.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.168896 restraints weight = 4372.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170146 restraints weight = 3480.136| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.6089 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= 0.117 Angle : 0.761 17.073 11960 Z= 0.340 Chirality : 0.044 0.253 1384 Planarity : 0.005 0.093 1497 Dihedral : 4.602 23.160 1139 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -2.86 (0.24), residues: 1017 helix: 0.26 (0.45), residues: 128 sheet: -1.68 (0.38), residues: 186 loop : -2.56 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 90 TYR 0.029 0.002 TYR A 52 PHE 0.011 0.001 PHE B 228 TRP 0.017 0.002 TRP A 279 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8754) covalent geometry : angle 0.74724 / 0.34 (11874) SS BOND : bond 0.00165 / 0.08 ( 13) SS BOND : angle 1.13273 / 0.67 ( 26) hydrogen bonds : bond 0.03287 / 2.18 ( 130) hydrogen bonds : angle 4.73642 / 3.52 ( 351) link_BETA1-3 : bond 0.01006 / 0.53 ( 1) link_BETA1-3 : angle 2.39457 / 1.12 ( 3) link_BETA1-4 : bond 0.00430 / 0.25 ( 11) link_BETA1-4 : angle 1.56652 / 0.92 ( 33) link_NAG-ASN : bond 0.00343 / 0.21 ( 8) link_NAG-ASN : angle 2.55593 / 1.37 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.97 seconds wall clock time: 27 minutes 23.71 seconds (1643.71 seconds total)