Starting phenix.real_space_refine on Thu May 15 11:20:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_44434_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_44434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_44434.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_44434_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcq_44434/05_2025/9bcq_44434_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.67, per 1000 atoms: 0.50 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: 3.80 Conformation dependent library (CDL) restraints added in 970.3 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: 1.14 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: 4.37 Time building geometry restraints manager: 4.47 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 425 or resid \ 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 425 or resid 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: 0.210 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: 0.220 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.940 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP B 146 HIS 0.006 0.001 HIS B 322 PHE 0.015 0.002 PHE B 172 TYR 0.008 0.001 TYR A 154 ARG 0.011 0.001 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 5) link_NAG-ASN : angle 2.93546 ( 15) link_BETA1-4 : bond 0.01323 ( 4) link_BETA1-4 : angle 5.88081 ( 12) link_ALPHA1-3 : bond 0.00352 ( 1) link_ALPHA1-3 : angle 4.94935 ( 3) hydrogen bonds : bond 0.20076 ( 260) hydrogen bonds : angle 8.33046 ( 756) SS BOND : bond 0.00607 ( 5) SS BOND : angle 0.99588 ( 10) covalent geometry : bond 0.00635 ( 7120) covalent geometry : angle 0.71287 ( 9701) *********************** 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 : 1.001 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.5164 time to fit residues: 45.6752 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.079891 restraints weight = 26741.109| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.59 r_work: 0.2587 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7135 Z= 0.194 Angle : 0.666 10.606 9741 Z= 0.330 Chirality : 0.063 1.372 1075 Planarity : 0.006 0.075 1257 Dihedral : 9.093 102.672 1167 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.57 % Allowed : 2.72 % Favored : 96.71 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 868 helix: 0.32 (0.29), residues: 300 sheet: -0.90 (0.40), residues: 164 loop : -1.08 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 146 HIS 0.006 0.001 HIS B 322 PHE 0.018 0.001 PHE B 219 TYR 0.020 0.001 TYR B 154 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 5) link_NAG-ASN : angle 2.24574 ( 15) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 3.60437 ( 12) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 4.06813 ( 3) hydrogen bonds : bond 0.05233 ( 260) hydrogen bonds : angle 5.58275 ( 756) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.79799 ( 10) covalent geometry : bond 0.00469 ( 7120) covalent geometry : angle 0.64434 ( 9701) *********************** 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 68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: B 373 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8743 (mm-30) outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.5580 time to fit residues: 46.7419 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 : 1.032 ------------------------------------------------------------------------------- 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 44 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.081021 restraints weight = 26600.110| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.81 r_work: 0.2625 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7135 Z= 0.118 Angle : 0.592 10.518 9741 Z= 0.289 Chirality : 0.061 1.358 1075 Planarity : 0.005 0.058 1257 Dihedral : 8.325 100.111 1167 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.43 % Allowed : 4.58 % Favored : 94.99 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 868 helix: 0.74 (0.30), residues: 304 sheet: -1.01 (0.39), residues: 164 loop : -1.01 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.009 0.001 PHE B 219 TYR 0.016 0.001 TYR B 154 ARG 0.002 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 5) link_NAG-ASN : angle 2.24899 ( 15) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 3.25379 ( 12) link_ALPHA1-3 : bond 0.01185 ( 1) link_ALPHA1-3 : angle 3.95303 ( 3) hydrogen bonds : bond 0.04309 ( 260) hydrogen bonds : angle 5.08081 ( 756) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.58149 ( 10) covalent geometry : bond 0.00275 ( 7120) covalent geometry : angle 0.57094 ( 9701) *********************** 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 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8267 (m-40) cc_final: 0.7975 (m-40) REVERT: B 373 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8580 (mm-30) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 0.5048 time to fit residues: 42.2106 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 : 1.033 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.095693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.080470 restraints weight = 26405.402| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.68 r_work: 0.2638 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1136 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= 0.124 Angle : 0.582 10.680 9741 Z= 0.282 Chirality : 0.061 1.372 1075 Planarity : 0.004 0.054 1257 Dihedral : 8.009 96.657 1167 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.43 % Allowed : 6.01 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 868 helix: 1.05 (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 TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.012 0.001 PHE B 219 TYR 0.016 0.001 TYR B 154 ARG 0.001 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 2.02909 ( 15) link_BETA1-4 : bond 0.00317 ( 4) link_BETA1-4 : angle 3.17467 ( 12) link_ALPHA1-3 : bond 0.01015 ( 1) link_ALPHA1-3 : angle 4.01371 ( 3) hydrogen bonds : bond 0.03907 ( 260) hydrogen bonds : angle 4.78632 ( 756) SS BOND : bond 0.00313 ( 5) SS BOND : angle 0.59036 ( 10) covalent geometry : bond 0.00298 ( 7120) covalent geometry : angle 0.56208 ( 9701) *********************** 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 : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8127 (m-40) cc_final: 0.7846 (m-40) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.4944 time to fit residues: 41.1699 Evaluate side-chains 63 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 43 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.082623 restraints weight = 26334.813| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.70 r_work: 0.2670 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7135 Z= 0.090 Angle : 0.546 10.476 9741 Z= 0.264 Chirality : 0.060 1.355 1075 Planarity : 0.004 0.050 1257 Dihedral : 7.482 96.232 1167 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.72 % Allowed : 7.30 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 868 helix: 1.24 (0.30), residues: 308 sheet: -1.14 (0.39), residues: 164 loop : -0.73 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.010 0.001 PHE B 172 TYR 0.014 0.001 TYR B 154 ARG 0.002 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 2.14025 ( 15) link_BETA1-4 : bond 0.00255 ( 4) link_BETA1-4 : angle 2.87831 ( 12) link_ALPHA1-3 : bond 0.01089 ( 1) link_ALPHA1-3 : angle 4.08868 ( 3) hydrogen bonds : bond 0.03479 ( 260) hydrogen bonds : angle 4.56892 ( 756) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.52952 ( 10) covalent geometry : bond 0.00209 ( 7120) covalent geometry : angle 0.52556 ( 9701) *********************** 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 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7891 (tt0) cc_final: 0.7134 (mt-10) REVERT: B 55 ASN cc_start: 0.8015 (m-40) cc_final: 0.7799 (m-40) REVERT: B 334 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7576 (mt-10) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.4829 time to fit residues: 41.5443 Evaluate side-chains 65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU 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 79 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.095901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.080542 restraints weight = 26412.147| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 1.69 r_work: 0.2610 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1318 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= 0.161 Angle : 0.585 10.677 9741 Z= 0.283 Chirality : 0.062 1.385 1075 Planarity : 0.005 0.054 1257 Dihedral : 7.603 89.927 1167 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.57 % Allowed : 8.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 868 helix: 1.20 (0.30), residues: 308 sheet: -1.12 (0.39), residues: 164 loop : -0.76 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 146 HIS 0.006 0.001 HIS B 322 PHE 0.013 0.001 PHE B 219 TYR 0.013 0.001 TYR B 154 ARG 0.003 0.000 ARG B 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 5) link_NAG-ASN : angle 1.99984 ( 15) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 3.27841 ( 12) link_ALPHA1-3 : bond 0.01063 ( 1) link_ALPHA1-3 : angle 3.99861 ( 3) hydrogen bonds : bond 0.03954 ( 260) hydrogen bonds : angle 4.62163 ( 756) SS BOND : bond 0.00407 ( 5) SS BOND : angle 0.66250 ( 10) covalent geometry : bond 0.00396 ( 7120) covalent geometry : angle 0.56503 ( 9701) *********************** 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 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7934 (tt0) cc_final: 0.7172 (mt-10) REVERT: B 55 ASN cc_start: 0.8070 (m-40) cc_final: 0.7841 (m-40) REVERT: B 334 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7777 (mt-10) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.5118 time to fit residues: 44.5411 Evaluate side-chains 68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.093950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.078596 restraints weight = 26782.926| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 1.69 r_work: 0.2571 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7135 Z= 0.214 Angle : 0.629 10.552 9741 Z= 0.306 Chirality : 0.064 1.392 1075 Planarity : 0.005 0.054 1257 Dihedral : 7.873 83.489 1167 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 868 helix: 1.08 (0.30), residues: 304 sheet: -1.10 (0.39), residues: 164 loop : -0.93 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 146 HIS 0.006 0.001 HIS B 322 PHE 0.017 0.001 PHE B 219 TYR 0.011 0.001 TYR B 154 ARG 0.003 0.000 ARG B 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 2.03573 ( 15) link_BETA1-4 : bond 0.00434 ( 4) link_BETA1-4 : angle 3.71478 ( 12) link_ALPHA1-3 : bond 0.01082 ( 1) link_ALPHA1-3 : angle 4.01885 ( 3) hydrogen bonds : bond 0.04444 ( 260) hydrogen bonds : angle 4.76945 ( 756) SS BOND : bond 0.00494 ( 5) SS BOND : angle 0.79805 ( 10) covalent geometry : bond 0.00532 ( 7120) covalent geometry : angle 0.60695 ( 9701) *********************** 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 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7982 (tt0) cc_final: 0.7221 (mt-10) REVERT: B 55 ASN cc_start: 0.8202 (m-40) cc_final: 0.7951 (m-40) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.4820 time to fit residues: 41.2646 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 : 0.981 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.080056 restraints weight = 26577.547| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.69 r_work: 0.2600 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7135 Z= 0.150 Angle : 0.591 10.433 9741 Z= 0.286 Chirality : 0.062 1.367 1075 Planarity : 0.005 0.052 1257 Dihedral : 7.573 83.112 1167 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.72 % Allowed : 8.58 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.29), residues: 868 helix: 1.08 (0.30), residues: 308 sheet: -1.13 (0.40), residues: 164 loop : -0.86 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.012 0.001 PHE B 219 TYR 0.013 0.001 TYR B 154 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 5) link_NAG-ASN : angle 2.05071 ( 15) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 3.44494 ( 12) link_ALPHA1-3 : bond 0.01136 ( 1) link_ALPHA1-3 : angle 4.21762 ( 3) hydrogen bonds : bond 0.04001 ( 260) hydrogen bonds : angle 4.64780 ( 756) SS BOND : bond 0.00363 ( 5) SS BOND : angle 0.69938 ( 10) covalent geometry : bond 0.00372 ( 7120) covalent geometry : angle 0.56930 ( 9701) *********************** 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 68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7953 (tt0) cc_final: 0.7200 (mt-10) REVERT: B 55 ASN cc_start: 0.8152 (m-40) cc_final: 0.7878 (m-40) REVERT: B 373 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8486 (mm-30) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.4796 time to fit residues: 40.9419 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 : 0.961 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.081955 restraints weight = 25966.364| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.71 r_work: 0.2625 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7135 Z= 0.099 Angle : 0.555 10.571 9741 Z= 0.267 Chirality : 0.060 1.376 1075 Planarity : 0.004 0.050 1257 Dihedral : 7.046 81.094 1167 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.43 % Allowed : 8.87 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.30), residues: 868 helix: 1.31 (0.31), residues: 308 sheet: -1.18 (0.39), residues: 164 loop : -0.69 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 18 HIS 0.005 0.001 HIS B 322 PHE 0.010 0.001 PHE B 172 TYR 0.014 0.001 TYR B 154 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 2.07578 ( 15) link_BETA1-4 : bond 0.00238 ( 4) link_BETA1-4 : angle 3.02249 ( 12) link_ALPHA1-3 : bond 0.01247 ( 1) link_ALPHA1-3 : angle 4.36663 ( 3) hydrogen bonds : bond 0.03480 ( 260) hydrogen bonds : angle 4.47879 ( 756) SS BOND : bond 0.00303 ( 5) SS BOND : angle 0.65358 ( 10) covalent geometry : bond 0.00238 ( 7120) covalent geometry : angle 0.53344 ( 9701) *********************** 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 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7855 (tt0) cc_final: 0.7107 (mt-10) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.4837 time to fit residues: 40.9373 Evaluate side-chains 65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.080816 restraints weight = 26263.214| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.73 r_work: 0.2600 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1479 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= 0.135 Angle : 0.575 10.626 9741 Z= 0.276 Chirality : 0.061 1.377 1075 Planarity : 0.005 0.053 1257 Dihedral : 6.909 72.160 1167 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 9.44 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.30), residues: 868 helix: 1.29 (0.30), residues: 308 sheet: -1.14 (0.40), residues: 164 loop : -0.69 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.011 0.001 PHE B 219 TYR 0.013 0.001 TYR B 154 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 5) link_NAG-ASN : angle 2.01750 ( 15) link_BETA1-4 : bond 0.00306 ( 4) link_BETA1-4 : angle 3.19012 ( 12) link_ALPHA1-3 : bond 0.01256 ( 1) link_ALPHA1-3 : angle 4.18659 ( 3) hydrogen bonds : bond 0.03750 ( 260) hydrogen bonds : angle 4.49498 ( 756) SS BOND : bond 0.00354 ( 5) SS BOND : angle 0.65686 ( 10) covalent geometry : bond 0.00335 ( 7120) covalent geometry : angle 0.55378 ( 9701) ********************** 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 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7878 (tt0) cc_final: 0.7127 (mt-10) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.4747 time to fit residues: 40.5407 Evaluate side-chains 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.082469 restraints weight = 26300.588| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.66 r_work: 0.2669 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1504 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= 0.129 Angle : 0.572 10.519 9741 Z= 0.275 Chirality : 0.061 1.382 1075 Planarity : 0.004 0.052 1257 Dihedral : 6.191 54.317 1167 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.43 % Allowed : 9.44 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 868 helix: 1.31 (0.30), residues: 308 sheet: -1.12 (0.40), residues: 164 loop : -0.69 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.005 0.001 HIS B 322 PHE 0.010 0.001 PHE B 219 TYR 0.013 0.001 TYR B 154 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 5) link_NAG-ASN : angle 2.04662 ( 15) link_BETA1-4 : bond 0.00278 ( 4) link_BETA1-4 : angle 3.07169 ( 12) link_ALPHA1-3 : bond 0.01714 ( 1) link_ALPHA1-3 : angle 3.88364 ( 3) hydrogen bonds : bond 0.03705 ( 260) hydrogen bonds : angle 4.46950 ( 756) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.65501 ( 10) covalent geometry : bond 0.00315 ( 7120) covalent geometry : angle 0.55234 ( 9701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5859.02 seconds wall clock time: 101 minutes 5.28 seconds (6065.28 seconds total)