Starting phenix.real_space_refine on Fri Jul 3 08:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcq_44434/07_2026/9bcq_44434.map" } resolution = 3.1 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= 0.005 sd= 0.224 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: 6 Type Number sf(0) Gaussians S 29 5.16 5 Cl 2 4.86 5 C 4426 2.51 5 N 1189 2.21 5 O 1289 1.98 5 H 6466 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 13401 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6460 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6476 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 326 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.66, per 1000 atoms: 0.20 Number of scatterers: 13401 At special positions: 0 Unit cell: (101.764, 68.2038, 89.8558, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 29 16.00 O 1289 8.00 N 1189 7.00 C 4426 6.00 H 6466 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 23 " 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 ALPHA1-3 " NAG G 2 " - " MAN G 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B1102 " - " ASN B 354 " " NAG D 1 " - " ASN A 13 " " NAG E 1 " - " ASN A 395 " " NAG F 1 " - " ASN B 13 " " NAG G 1 " - " ASN B 395 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 536.1 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 39.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 19 through 34 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.708A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.697A pdb=" N TYR A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.670A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 338 removed outlier: 3.525A pdb=" N ALA A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.665A pdb=" N GLN A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix removed outlier: 3.737A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.789A pdb=" N LEU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.718A pdb=" N PHE B 114 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 4.038A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.091A pdb=" N TYR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.839A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.710A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 338 Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.573A pdb=" N ARG B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.662A pdb=" N GLY C 16 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 18' Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 removed outlier: 6.060A pdb=" N LEU A 3 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL A 49 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 5 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY A 51 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL A 7 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 80 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 5.797A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 189 removed outlier: 3.695A pdb=" N ASP A 184 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 400 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.488A pdb=" N LEU B 3 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 49 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY B 51 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL B 7 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 80 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.075A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 189 removed outlier: 3.535A pdb=" N ALA B 150 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 279 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 392 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP B 380 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 390 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.612A pdb=" N ARG B 355 " --> pdb=" O ILE B 366 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6459 1.04 - 1.23: 249 1.23 - 1.43: 2844 1.43 - 1.63: 3990 1.63 - 1.82: 44 Bond restraints: 13586 Sorted by residual: bond pdb=" C GLU A 373 " pdb=" O GLU A 373 " ideal model delta sigma weight residual 1.236 1.182 0.053 1.17e-02 7.31e+03 2.09e+01 bond pdb=" C GLU B 373 " pdb=" O GLU B 373 " ideal model delta sigma weight residual 1.236 1.187 0.048 1.21e-02 6.83e+03 1.61e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CD GLU A 373 " pdb=" OE2 GLU A 373 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.19e+00 bond pdb=" N GLU A 373 " pdb=" H GLU A 373 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.67e+00 ... (remaining 13581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.11: 24343 7.11 - 14.21: 4 14.21 - 21.32: 1 21.32 - 28.42: 7 28.42 - 35.53: 12 Bond angle restraints: 24367 Sorted by residual: angle pdb=" N TRP B 146 " pdb=" CA TRP B 146 " pdb=" HA TRP B 146 " ideal model delta sigma weight residual 110.00 74.47 35.53 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C ARG B 148 " pdb=" CA ARG B 148 " pdb=" HA ARG B 148 " ideal model delta sigma weight residual 109.00 73.97 35.03 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ARG B 148 " pdb=" CA ARG B 148 " pdb=" HA ARG B 148 " ideal model delta sigma weight residual 110.00 75.29 34.71 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C TRP B 146 " pdb=" CA TRP B 146 " pdb=" HA TRP B 146 " ideal model delta sigma weight residual 109.00 74.38 34.62 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB TRP B 146 " pdb=" CA TRP B 146 " pdb=" HA TRP B 146 " ideal model delta sigma weight residual 109.00 76.50 32.50 3.00e+00 1.11e-01 1.17e+02 ... (remaining 24362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 6175 23.11 - 46.22: 371 46.22 - 69.33: 85 69.33 - 92.43: 11 92.43 - 115.54: 1 Dihedral angle restraints: 6643 sinusoidal: 3626 harmonic: 3017 Sorted by residual: dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 156.48 23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU B 82 " pdb=" C LEU B 82 " pdb=" N GLY B 83 " pdb=" CA GLY B 83 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LYS B 117 " pdb=" C LYS B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1071 0.287 - 0.575: 3 0.575 - 0.862: 0 0.862 - 1.150: 0 1.150 - 1.437: 1 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL B 183 " pdb=" CA VAL B 183 " pdb=" CG1 VAL B 183 " pdb=" CG2 VAL B 183 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.16e+01 chirality pdb=" CA ARG B 148 " pdb=" N ARG B 148 " pdb=" C ARG B 148 " pdb=" CB ARG B 148 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.13 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1072 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 317 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO B 318 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 372 " -0.020 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" N GLU A 373 " 0.062 2.00e-02 2.50e+03 pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 pdb=" H GLU A 373 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 317 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 318 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.044 5.00e-02 4.00e+02 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 672 2.19 - 2.79: 26346 2.79 - 3.40: 36204 3.40 - 4.00: 49641 4.00 - 4.60: 76973 Nonbonded interactions: 189836 Sorted by model distance: nonbonded pdb=" H ARG B 148 " pdb=" HA ARG B 148 " model vdw 1.588 1.816 nonbonded pdb=" H TRP B 146 " pdb=" HA TRP B 146 " model vdw 1.599 1.816 nonbonded pdb=" O PRO A 204 " pdb="HH12 ARG A 208 " model vdw 1.632 2.450 nonbonded pdb=" HB3 MET A 203 " pdb=" HG2 MET A 203 " model vdw 1.645 1.952 nonbonded pdb=" HB2 MET A 203 " pdb=" HG3 MET A 203 " model vdw 1.655 1.952 ... (remaining 189831 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 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 36 through 147 or (resid 148 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA )) or resid 149 through 179 or (resid 180 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 181 through 204 or (resid 205 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 206 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name OE1 or na \ me OE2 or name H or name HA )) or resid 293 through 404 or (resid 405 and (name \ N or name CA or name C or name O or name CB or name OG or name H or name HA )) o \ r resid 406 through 422 or (resid 423 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA )) or resid 424 through 1101)) selection = (chain 'B' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 76 through 160 or (resid \ 161 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name OE2 or name H or name HA )) or resid 162 through 200 or (res \ id 201 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or resi \ d 202 through 227 or (resid 228 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) or r \ esid 229 through 285 or (resid 286 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 287 through 302 or (resid 303 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name OE1 \ or name OE2 or name H or name HA )) or resid 304 through 383 or (resid 384 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 385 through 407 or (resid 408 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 409 through 1101)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.006 0.064 7135 Z= 0.279 Angle : 0.755 16.161 9741 Z= 0.384 Chirality : 0.067 1.437 1075 Planarity : 0.006 0.103 1257 Dihedral : 14.486 115.542 2697 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.28), residues: 868 helix: -0.33 (0.29), residues: 300 sheet: -0.41 (0.44), residues: 148 loop : -1.13 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 389 TYR 0.008 0.001 TYR A 154 PHE 0.015 0.002 PHE B 172 TRP 0.026 0.002 TRP B 146 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.28 ( 7120) covalent geometry : angle 0.71287 / 0.38 ( 9701) SS BOND : bond 0.00607 / 0.36 ( 5) SS BOND : angle 0.99588 / 0.64 ( 10) hydrogen bonds : bond 0.20076 / 13.15 ( 260) hydrogen bonds : angle 8.33046 / 5.95 ( 756) link_ALPHA1-3 : bond 0.00352 / 0.22 ( 1) link_ALPHA1-3 : angle 4.94935 / 2.11 ( 3) link_BETA1-4 : bond 0.01323 / 0.94 ( 4) link_BETA1-4 : angle 5.88081 / 2.70 ( 12) link_NAG-ASN : bond 0.00531 / 0.41 ( 5) link_NAG-ASN : angle 2.93546 / 2.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2253 time to fit residues: 20.0540 Evaluate side-chains 58 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.080643 restraints weight = 26796.077| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 1.58 r_work: 0.2600 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7135 Z= 0.148 Angle : 0.639 10.557 9741 Z= 0.318 Chirality : 0.062 1.373 1075 Planarity : 0.005 0.076 1257 Dihedral : 9.060 104.870 1167 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.57 % Allowed : 2.29 % Favored : 97.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.28), residues: 868 helix: 0.42 (0.29), residues: 300 sheet: -0.83 (0.40), residues: 164 loop : -1.03 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.018 0.001 TYR B 154 PHE 0.015 0.001 PHE B 219 TRP 0.016 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7120) covalent geometry : angle 0.61761 / 0.31 ( 9701) SS BOND : bond 0.00322 / 0.20 ( 5) SS BOND : angle 0.69592 / 0.46 ( 10) hydrogen bonds : bond 0.05519 / 3.74 ( 260) hydrogen bonds : angle 5.65257 / 4.08 ( 756) link_ALPHA1-3 : bond 0.01045 / 0.65 ( 1) link_ALPHA1-3 : angle 4.03819 / 1.82 ( 3) link_BETA1-4 : bond 0.00326 / 0.23 ( 4) link_BETA1-4 : angle 3.53698 / 1.67 ( 12) link_NAG-ASN : bond 0.00246 / 0.17 ( 5) link_NAG-ASN : angle 2.27131 / 1.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8392 (m-40) cc_final: 0.8005 (m-40) outliers start: 4 outliers final: 4 residues processed: 67 average time/residue: 0.2444 time to fit residues: 20.9323 Evaluate side-chains 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.0020 chunk 61 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.081568 restraints weight = 26428.699| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.82 r_work: 0.2647 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7135 Z= 0.111 Angle : 0.586 10.509 9741 Z= 0.286 Chirality : 0.061 1.360 1075 Planarity : 0.005 0.059 1257 Dihedral : 8.263 100.787 1167 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.29 % Allowed : 4.15 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.29), residues: 868 helix: 0.83 (0.30), residues: 304 sheet: -1.01 (0.40), residues: 164 loop : -0.96 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.016 0.001 TYR B 154 PHE 0.008 0.001 PHE B 219 TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7120) covalent geometry : angle 0.56505 / 0.28 ( 9701) SS BOND : bond 0.00231 / 0.15 ( 5) SS BOND : angle 0.52545 / 0.35 ( 10) hydrogen bonds : bond 0.04290 / 2.96 ( 260) hydrogen bonds : angle 5.07698 / 3.68 ( 756) link_ALPHA1-3 : bond 0.01125 / 0.70 ( 1) link_ALPHA1-3 : angle 3.94163 / 1.79 ( 3) link_BETA1-4 : bond 0.00271 / 0.18 ( 4) link_BETA1-4 : angle 3.15522 / 1.53 ( 12) link_NAG-ASN : bond 0.00242 / 0.16 ( 5) link_NAG-ASN : angle 2.22569 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8232 (m-40) cc_final: 0.7925 (m-40) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.1946 time to fit residues: 17.1792 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.080316 restraints weight = 26440.577| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.69 r_work: 0.2622 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7135 Z= 0.133 Angle : 0.586 10.572 9741 Z= 0.286 Chirality : 0.062 1.380 1075 Planarity : 0.005 0.055 1257 Dihedral : 7.966 96.063 1167 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.43 % Allowed : 5.44 % Favored : 94.13 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.29), residues: 868 helix: 1.06 (0.30), residues: 304 sheet: -1.10 (0.39), residues: 164 loop : -0.91 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 11 TYR 0.015 0.001 TYR B 154 PHE 0.011 0.001 PHE B 219 TRP 0.018 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 7120) covalent geometry : angle 0.56557 / 0.28 ( 9701) SS BOND : bond 0.00394 / 0.25 ( 5) SS BOND : angle 0.57527 / 0.36 ( 10) hydrogen bonds : bond 0.04041 / 2.77 ( 260) hydrogen bonds : angle 4.79473 / 3.47 ( 756) link_ALPHA1-3 : bond 0.01118 / 0.70 ( 1) link_ALPHA1-3 : angle 3.89180 / 1.81 ( 3) link_BETA1-4 : bond 0.00312 / 0.21 ( 4) link_BETA1-4 : angle 3.24344 / 1.61 ( 12) link_NAG-ASN : bond 0.00213 / 0.15 ( 5) link_NAG-ASN : angle 2.04466 / 1.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8094 (m-40) cc_final: 0.7823 (m-40) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.1998 time to fit residues: 16.8392 Evaluate side-chains 64 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.095644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.080430 restraints weight = 26572.995| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.68 r_work: 0.2617 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7135 Z= 0.145 Angle : 0.583 10.653 9741 Z= 0.283 Chirality : 0.062 1.375 1075 Planarity : 0.005 0.054 1257 Dihedral : 7.857 93.312 1167 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 6.44 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.29), residues: 868 helix: 1.13 (0.30), residues: 304 sheet: -1.12 (0.39), residues: 164 loop : -0.88 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.014 0.001 TYR B 154 PHE 0.012 0.001 PHE B 219 TRP 0.015 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 7120) covalent geometry : angle 0.56214 / 0.28 ( 9701) SS BOND : bond 0.00373 / 0.23 ( 5) SS BOND : angle 0.61073 / 0.38 ( 10) hydrogen bonds : bond 0.04019 / 2.76 ( 260) hydrogen bonds : angle 4.73469 / 3.42 ( 756) link_ALPHA1-3 : bond 0.01080 / 0.68 ( 1) link_ALPHA1-3 : angle 4.00314 / 1.85 ( 3) link_BETA1-4 : bond 0.00322 / 0.22 ( 4) link_BETA1-4 : angle 3.29199 / 1.62 ( 12) link_NAG-ASN : bond 0.00176 / 0.12 ( 5) link_NAG-ASN : angle 2.06796 / 1.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7962 (tt0) cc_final: 0.7200 (mt-10) REVERT: B 55 ASN cc_start: 0.8117 (m-40) cc_final: 0.7856 (m-40) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.1982 time to fit residues: 17.6770 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.080162 restraints weight = 26576.414| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.69 r_work: 0.2605 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7135 Z= 0.145 Angle : 0.583 10.544 9741 Z= 0.283 Chirality : 0.062 1.372 1075 Planarity : 0.005 0.053 1257 Dihedral : 7.734 90.283 1167 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.86 % Allowed : 7.87 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.29), residues: 868 helix: 1.20 (0.30), residues: 304 sheet: -1.14 (0.39), residues: 164 loop : -0.86 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.014 0.001 TYR B 154 PHE 0.012 0.001 PHE B 219 TRP 0.015 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 ( 7120) covalent geometry : angle 0.56215 / 0.28 ( 9701) SS BOND : bond 0.00372 / 0.23 ( 5) SS BOND : angle 0.61086 / 0.38 ( 10) hydrogen bonds : bond 0.03970 / 2.74 ( 260) hydrogen bonds : angle 4.68008 / 3.37 ( 756) link_ALPHA1-3 : bond 0.01095 / 0.68 ( 1) link_ALPHA1-3 : angle 4.07220 / 1.91 ( 3) link_BETA1-4 : bond 0.00324 / 0.22 ( 4) link_BETA1-4 : angle 3.31182 / 1.63 ( 12) link_NAG-ASN : bond 0.00185 / 0.12 ( 5) link_NAG-ASN : angle 2.04245 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7957 (tt0) cc_final: 0.7203 (mt-10) REVERT: B 55 ASN cc_start: 0.8109 (m-40) cc_final: 0.7852 (m-40) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.2066 time to fit residues: 18.6894 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.081429 restraints weight = 26255.508| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.68 r_work: 0.2636 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7135 Z= 0.104 Angle : 0.557 10.534 9741 Z= 0.269 Chirality : 0.061 1.365 1075 Planarity : 0.004 0.051 1257 Dihedral : 7.460 90.269 1167 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.57 % Allowed : 8.30 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.29), residues: 868 helix: 1.28 (0.30), residues: 308 sheet: -1.16 (0.39), residues: 164 loop : -0.76 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.014 0.001 TYR B 154 PHE 0.010 0.001 PHE B 172 TRP 0.011 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 7120) covalent geometry : angle 0.53662 / 0.26 ( 9701) SS BOND : bond 0.00277 / 0.17 ( 5) SS BOND : angle 0.56128 / 0.37 ( 10) hydrogen bonds : bond 0.03625 / 2.50 ( 260) hydrogen bonds : angle 4.55392 / 3.29 ( 756) link_ALPHA1-3 : bond 0.01130 / 0.71 ( 1) link_ALPHA1-3 : angle 4.18731 / 1.95 ( 3) link_BETA1-4 : bond 0.00253 / 0.17 ( 4) link_BETA1-4 : angle 3.09019 / 1.51 ( 12) link_NAG-ASN : bond 0.00220 / 0.15 ( 5) link_NAG-ASN : angle 2.05566 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7930 (tt0) cc_final: 0.7181 (mt-10) REVERT: B 55 ASN cc_start: 0.8064 (m-40) cc_final: 0.7843 (m-40) REVERT: B 298 LYS cc_start: 0.8075 (mttt) cc_final: 0.7799 (mmtp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1918 time to fit residues: 15.6728 Evaluate side-chains 63 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.080409 restraints weight = 26205.420| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.69 r_work: 0.2598 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7135 Z= 0.153 Angle : 0.582 10.647 9741 Z= 0.282 Chirality : 0.062 1.386 1075 Planarity : 0.005 0.053 1257 Dihedral : 7.512 86.459 1167 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.72 % Allowed : 8.15 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.29), residues: 868 helix: 1.23 (0.30), residues: 308 sheet: -1.17 (0.39), residues: 164 loop : -0.80 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.013 0.001 TYR B 154 PHE 0.012 0.001 PHE B 219 TRP 0.015 0.001 TRP B 146 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 ( 7120) covalent geometry : angle 0.56101 / 0.28 ( 9701) SS BOND : bond 0.00386 / 0.24 ( 5) SS BOND : angle 0.62565 / 0.39 ( 10) hydrogen bonds : bond 0.03937 / 2.70 ( 260) hydrogen bonds : angle 4.59862 / 3.32 ( 756) link_ALPHA1-3 : bond 0.01076 / 0.67 ( 1) link_ALPHA1-3 : angle 4.05455 / 1.90 ( 3) link_BETA1-4 : bond 0.00318 / 0.22 ( 4) link_BETA1-4 : angle 3.32051 / 1.64 ( 12) link_NAG-ASN : bond 0.00168 / 0.12 ( 5) link_NAG-ASN : angle 2.02083 / 1.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7876 (tt0) cc_final: 0.7114 (mt-10) REVERT: B 55 ASN cc_start: 0.8075 (m-40) cc_final: 0.7830 (m-40) REVERT: B 298 LYS cc_start: 0.8070 (mttt) cc_final: 0.7794 (mmtp) outliers start: 5 outliers final: 5 residues processed: 67 average time/residue: 0.2057 time to fit residues: 18.1574 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 295 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.080394 restraints weight = 26547.504| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.70 r_work: 0.2606 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7135 Z= 0.135 Angle : 0.573 10.563 9741 Z= 0.277 Chirality : 0.061 1.377 1075 Planarity : 0.005 0.052 1257 Dihedral : 7.379 84.950 1167 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 8.15 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.29), residues: 868 helix: 1.26 (0.30), residues: 308 sheet: -1.16 (0.39), residues: 164 loop : -0.77 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.013 0.001 TYR B 154 PHE 0.011 0.001 PHE B 219 TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.13 ( 7120) covalent geometry : angle 0.55169 / 0.27 ( 9701) SS BOND : bond 0.00351 / 0.22 ( 5) SS BOND : angle 0.61072 / 0.39 ( 10) hydrogen bonds : bond 0.03814 / 2.62 ( 260) hydrogen bonds : angle 4.55192 / 3.29 ( 756) link_ALPHA1-3 : bond 0.01130 / 0.71 ( 1) link_ALPHA1-3 : angle 4.12201 / 1.94 ( 3) link_BETA1-4 : bond 0.00295 / 0.21 ( 4) link_BETA1-4 : angle 3.24465 / 1.59 ( 12) link_NAG-ASN : bond 0.00180 / 0.12 ( 5) link_NAG-ASN : angle 2.03557 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7878 (tt0) cc_final: 0.7132 (mt-10) REVERT: B 55 ASN cc_start: 0.8070 (m-40) cc_final: 0.7830 (m-40) REVERT: B 298 LYS cc_start: 0.8102 (mttt) cc_final: 0.7845 (mmtp) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.2172 time to fit residues: 18.4749 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.081711 restraints weight = 26211.394| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.73 r_work: 0.2621 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7135 Z= 0.112 Angle : 0.557 10.323 9741 Z= 0.268 Chirality : 0.060 1.339 1075 Planarity : 0.004 0.051 1257 Dihedral : 7.016 80.707 1167 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 8.15 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.30), residues: 868 helix: 1.36 (0.31), residues: 308 sheet: -1.14 (0.39), residues: 164 loop : -0.68 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.013 0.001 TYR B 154 PHE 0.012 0.001 PHE B 172 TRP 0.011 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 ( 7120) covalent geometry : angle 0.53616 / 0.26 ( 9701) SS BOND : bond 0.00325 / 0.20 ( 5) SS BOND : angle 0.60864 / 0.39 ( 10) hydrogen bonds : bond 0.03585 / 2.47 ( 260) hydrogen bonds : angle 4.46013 / 3.22 ( 756) link_ALPHA1-3 : bond 0.01150 / 0.72 ( 1) link_ALPHA1-3 : angle 4.24209 / 1.97 ( 3) link_BETA1-4 : bond 0.00268 / 0.18 ( 4) link_BETA1-4 : angle 3.07269 / 1.50 ( 12) link_NAG-ASN : bond 0.00211 / 0.15 ( 5) link_NAG-ASN : angle 2.01830 / 1.38 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 408 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7892 (tt0) cc_final: 0.7169 (mt-10) REVERT: B 55 ASN cc_start: 0.8015 (m-40) cc_final: 0.7807 (m-40) REVERT: B 298 LYS cc_start: 0.8135 (mttt) cc_final: 0.7925 (mmtp) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.1993 time to fit residues: 17.9071 Evaluate side-chains 68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.082910 restraints weight = 26304.389| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.69 r_work: 0.2640 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7135 Z= 0.125 Angle : 0.568 10.715 9741 Z= 0.273 Chirality : 0.062 1.410 1075 Planarity : 0.004 0.052 1257 Dihedral : 6.775 72.041 1167 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 8.30 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.30), residues: 868 helix: 1.36 (0.31), residues: 308 sheet: -1.11 (0.39), residues: 164 loop : -0.68 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.013 0.001 TYR B 154 PHE 0.010 0.001 PHE B 219 TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.12 ( 7120) covalent geometry : angle 0.54717 / 0.27 ( 9701) SS BOND : bond 0.00334 / 0.20 ( 5) SS BOND : angle 0.61973 / 0.39 ( 10) hydrogen bonds : bond 0.03669 / 2.52 ( 260) hydrogen bonds : angle 4.46790 / 3.22 ( 756) link_ALPHA1-3 : bond 0.01248 / 0.78 ( 1) link_ALPHA1-3 : angle 4.19209 / 1.93 ( 3) link_BETA1-4 : bond 0.00282 / 0.19 ( 4) link_BETA1-4 : angle 3.09955 / 1.52 ( 12) link_NAG-ASN : bond 0.00177 / 0.12 ( 5) link_NAG-ASN : angle 2.02543 / 1.39 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.44 seconds wall clock time: 49 minutes 22.13 seconds (2962.13 seconds total)