Starting phenix.real_space_refine on Mon Apr 6 20:20:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5z_55599/04_2026/9t5z_55599_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5z_55599/04_2026/9t5z_55599.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/9t5z_55599/04_2026/9t5z_55599_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5z_55599/04_2026/9t5z_55599_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t5z_55599/04_2026/9t5z_55599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5z_55599/04_2026/9t5z_55599.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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 1 7.51 5 S 51 5.16 5 C 6715 2.51 5 N 1834 2.21 5 O 2146 1.98 5 H 10267 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21019 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 8540 Classifications: {'peptide': 567} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 539} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 5656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5656 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 344} Chain: "H" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3296 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 201} Chain: "L" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3297 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 202} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 2, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.83, per 1000 atoms: 0.18 Number of scatterers: 21019 At special positions: 0 Unit cell: (84.11, 129.4, 131.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 1 24.99 Ca 5 19.99 S 51 16.00 O 2146 8.00 N 1834 7.00 C 6715 6.00 H 10267 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 489 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 695 " distance=2.07 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 218 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B2004 " - " ASN B 190 " " NAG B2005 " - " ASN B 232 " " NAG C 1 " - " ASN A 718 " " NAG D 1 " - " ASN A 70 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 94 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 594.2 milliseconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 10.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'B' and resid 114 through 119 removed outlier: 4.155A pdb=" N ASP B 119 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.737A pdb=" N GLY B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 271 through 277 removed outlier: 4.308A pdb=" N ASN B 275 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 304 through 313 removed outlier: 3.558A pdb=" N TYR B 308 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 339 removed outlier: 3.700A pdb=" N VAL B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.830A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 206 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.268A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 214 No H-bonds generated for 'chain 'L' and resid 212 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.971A pdb=" N MET A 9 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.076A pdb=" N SER A 21 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 removed outlier: 7.389A pdb=" N GLN A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 80 removed outlier: 5.350A pdb=" N LEU A 87 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 110 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYS A 89 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE A 108 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU A 106 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 396 removed outlier: 3.754A pdb=" N ALA A 391 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 430 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 420 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER A 428 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN A 422 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TRP A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.243A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 491 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 512 removed outlier: 6.110A pdb=" N ASP A 521 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.769A pdb=" N GLY A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 694 through 698 Processing sheet with id=AB2, first strand: chain 'A' and resid 629 through 630 removed outlier: 3.707A pdb=" N LYS A 630 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 702 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 689 Processing sheet with id=AB4, first strand: chain 'B' and resid 62 through 66 removed outlier: 6.948A pdb=" N VAL B 81 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU B 420 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 83 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 76 through 77 removed outlier: 6.916A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 183 through 189 removed outlier: 5.055A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 188 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 105 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLY B 145 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 107 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY B 147 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B 109 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE B 149 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 111 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.617A pdb=" N VAL H 12 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU H 45 " --> pdb=" O PHE H 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 123 through 127 removed outlier: 6.083A pdb=" N TYR H 178 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 123 through 127 removed outlier: 6.083A pdb=" N TYR H 178 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 154 through 157 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.152A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN L 37 " --> pdb=" O THR L 46 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.133A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.320A pdb=" N TRP L 148 " --> pdb=" O ARG L 155 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS L 198 " --> pdb=" O SER L 203 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 203 " --> pdb=" O HIS L 198 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1011 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: 4.63 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.05: 10266 1.05 - 1.29: 1784 1.29 - 1.53: 7147 1.53 - 1.76: 1961 1.76 - 2.00: 70 Bond restraints: 21228 Sorted by residual: bond pdb=" CB CYS A 638 " pdb=" SG CYS A 638 " ideal model delta sigma weight residual 1.808 2.001 -0.193 3.30e-02 9.18e+02 3.43e+01 bond pdb=" C GLN A 575 " pdb=" N ASP A 576 " ideal model delta sigma weight residual 1.331 1.249 0.082 1.41e-02 5.03e+03 3.35e+01 bond pdb=" ND2 ASN B 94 " pdb="HD22 ASN B 94 " ideal model delta sigma weight residual 0.860 0.945 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CA CYS A 638 " pdb=" HA CYS A 638 " ideal model delta sigma weight residual 0.970 0.907 0.063 2.00e-02 2.50e+03 9.82e+00 bond pdb=" N VAL B 95 " pdb=" CA VAL B 95 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 ... (remaining 21223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.44: 38144 6.44 - 12.87: 33 12.87 - 19.31: 5 19.31 - 25.74: 5 25.74 - 32.18: 2 Bond angle restraints: 38189 Sorted by residual: angle pdb=" SG CYS A 705 " pdb=" CB CYS A 705 " pdb=" HB2 CYS A 705 " ideal model delta sigma weight residual 108.00 75.82 32.18 3.00e+00 1.11e-01 1.15e+02 angle pdb=" SG CYS A 705 " pdb=" CB CYS A 705 " pdb=" HB3 CYS A 705 " ideal model delta sigma weight residual 108.00 77.21 30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CA CYS A 705 " pdb=" CB CYS A 705 " pdb=" HB2 CYS A 705 " ideal model delta sigma weight residual 109.00 83.74 25.26 3.00e+00 1.11e-01 7.09e+01 angle pdb=" CA CYS A 695 " pdb=" CB CYS A 695 " pdb=" SG CYS A 695 " ideal model delta sigma weight residual 114.40 133.09 -18.69 2.30e+00 1.89e-01 6.61e+01 angle pdb=" CA CYS A 705 " pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " ideal model delta sigma weight residual 114.40 132.12 -17.72 2.30e+00 1.89e-01 5.94e+01 ... (remaining 38184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 9643 26.43 - 52.86: 604 52.86 - 79.29: 82 79.29 - 105.72: 34 105.72 - 132.15: 16 Dihedral angle restraints: 10379 sinusoidal: 5832 harmonic: 4547 Sorted by residual: dihedral pdb=" CB CYS H 218 " pdb=" SG CYS H 218 " pdb=" SG CYS L 214 " pdb=" CB CYS L 214 " ideal model delta sinusoidal sigma weight residual 93.00 168.55 -75.55 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS A 638 " pdb=" SG CYS A 638 " pdb=" SG CYS A 695 " pdb=" CB CYS A 695 " ideal model delta sinusoidal sigma weight residual 93.00 25.23 67.77 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CA SER A 82 " pdb=" C SER A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 10376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1401 0.066 - 0.132: 278 0.132 - 0.199: 33 0.199 - 0.265: 3 0.265 - 0.331: 2 Chirality restraints: 1717 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.39e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 94 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE A 706 " pdb=" CA ILE A 706 " pdb=" CG1 ILE A 706 " pdb=" CG2 ILE A 706 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1714 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 94 " -0.006 2.00e-02 2.50e+03 3.79e-01 2.16e+03 pdb=" CG ASN B 94 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN B 94 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 94 " -0.129 2.00e-02 2.50e+03 pdb="HD21 ASN B 94 " -0.507 2.00e-02 2.50e+03 pdb="HD22 ASN B 94 " 0.760 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.240 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" C7 NAG F 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 94 " -0.016 2.00e-02 2.50e+03 8.51e-02 1.09e+02 pdb=" CG ASN B 94 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 94 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 94 " 0.178 2.00e-02 2.50e+03 pdb="HD21 ASN B 94 " -0.101 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.031 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 11707 2.44 - 2.98: 46744 2.98 - 3.52: 54506 3.52 - 4.06: 75804 4.06 - 4.60: 107300 Nonbonded interactions: 296061 Sorted by model distance: nonbonded pdb=" HG SER H 183 " pdb="HD22 ASN L 137 " model vdw 1.904 2.100 nonbonded pdb=" HE1 TYR H 59 " pdb=" H ILE H 69 " model vdw 1.949 2.100 nonbonded pdb=" HE2 PHE B 346 " pdb=" H ASP H 100 " model vdw 1.949 2.100 nonbonded pdb=" HH TYR H 47 " pdb=" HD2 TYR H 50 " model vdw 1.960 2.100 nonbonded pdb=" H ASN A 611 " pdb="HH21 ARG A 636 " model vdw 1.966 2.100 ... (remaining 296056 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 'D' selection = chain 'E' } 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: 2.900 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: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 0.193 10993 Z= 0.265 Angle : 1.051 18.693 14965 Z= 0.533 Chirality : 0.054 0.331 1717 Planarity : 0.009 0.203 1926 Dihedral : 18.863 132.147 4291 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 1.36 % Allowed : 24.68 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.97 (0.22), residues: 1353 helix: -1.07 (0.44), residues: 107 sheet: -1.13 (0.21), residues: 531 loop : -1.43 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 99 TYR 0.023 0.002 TYR B 103 PHE 0.020 0.002 PHE L 36 TRP 0.023 0.002 TRP A 487 HIS 0.007 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00586 (10961) covalent geometry : angle 1.02099 (14884) SS BOND : bond 0.01109 ( 15) SS BOND : angle 3.64474 ( 30) hydrogen bonds : bond 0.13024 ( 374) hydrogen bonds : angle 7.80019 ( 1011) link_ALPHA1-3 : bond 0.01538 ( 2) link_ALPHA1-3 : angle 2.32520 ( 6) link_ALPHA1-6 : bond 0.00421 ( 2) link_ALPHA1-6 : angle 1.71439 ( 6) link_BETA1-4 : bond 0.01889 ( 7) link_BETA1-4 : angle 3.04333 ( 21) link_NAG-ASN : bond 0.04769 ( 6) link_NAG-ASN : angle 4.55781 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7068 (tp) REVERT: H 34 TRP cc_start: 0.7335 (m100) cc_final: 0.6695 (m100) REVERT: H 48 MET cc_start: 0.8876 (mtp) cc_final: 0.8650 (mtm) REVERT: H 81 GLN cc_start: 0.7415 (tp40) cc_final: 0.7062 (tm-30) REVERT: H 157 TRP cc_start: 0.6879 (m100) cc_final: 0.6440 (m100) REVERT: L 210 ASN cc_start: 0.7737 (m-40) cc_final: 0.7379 (m-40) outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.2668 time to fit residues: 42.3106 Evaluate side-chains 92 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 199 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 411 GLN A 422 ASN ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.129231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.088069 restraints weight = 62020.720| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.28 r_work: 0.3270 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10993 Z= 0.202 Angle : 0.714 15.580 14965 Z= 0.357 Chirality : 0.047 0.322 1717 Planarity : 0.006 0.138 1926 Dihedral : 12.086 111.332 1841 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.60 % Rotamer: Outliers : 2.47 % Allowed : 22.04 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.66 (0.22), residues: 1353 helix: -0.27 (0.47), residues: 107 sheet: -0.95 (0.21), residues: 533 loop : -1.28 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.020 0.001 TYR L 87 PHE 0.019 0.001 PHE B 93 TRP 0.012 0.002 TRP H 36 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00460 (10961) covalent geometry : angle 0.68834 (14884) SS BOND : bond 0.00654 ( 15) SS BOND : angle 2.00759 ( 30) hydrogen bonds : bond 0.03808 ( 374) hydrogen bonds : angle 6.40456 ( 1011) link_ALPHA1-3 : bond 0.01296 ( 2) link_ALPHA1-3 : angle 3.04270 ( 6) link_ALPHA1-6 : bond 0.00173 ( 2) link_ALPHA1-6 : angle 2.11586 ( 6) link_BETA1-4 : bond 0.00415 ( 7) link_BETA1-4 : angle 1.87276 ( 21) link_NAG-ASN : bond 0.00623 ( 6) link_NAG-ASN : angle 4.08902 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7253 (tt) REVERT: H 81 GLN cc_start: 0.7824 (tp40) cc_final: 0.7162 (tm-30) REVERT: H 157 TRP cc_start: 0.7014 (m100) cc_final: 0.6615 (m100) REVERT: H 211 LYS cc_start: 0.7346 (tppt) cc_final: 0.7138 (tppp) REVERT: L 89 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8066 (tp) REVERT: L 138 ASN cc_start: 0.8617 (m-40) cc_final: 0.8391 (m-40) outliers start: 29 outliers final: 16 residues processed: 107 average time/residue: 0.2726 time to fit residues: 40.1809 Evaluate side-chains 95 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 81 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.129353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086748 restraints weight = 61764.234| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.44 r_work: 0.3251 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10993 Z= 0.151 Angle : 0.663 14.238 14965 Z= 0.328 Chirality : 0.046 0.319 1717 Planarity : 0.005 0.132 1926 Dihedral : 9.825 108.511 1836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 2.72 % Allowed : 21.87 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.44 (0.22), residues: 1353 helix: 0.10 (0.49), residues: 107 sheet: -0.84 (0.21), residues: 529 loop : -1.14 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.015 0.001 TYR L 87 PHE 0.018 0.001 PHE B 93 TRP 0.013 0.001 TRP H 36 HIS 0.003 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00357 (10961) covalent geometry : angle 0.63829 (14884) SS BOND : bond 0.00617 ( 15) SS BOND : angle 1.97955 ( 30) hydrogen bonds : bond 0.03418 ( 374) hydrogen bonds : angle 6.05031 ( 1011) link_ALPHA1-3 : bond 0.00862 ( 2) link_ALPHA1-3 : angle 2.68964 ( 6) link_ALPHA1-6 : bond 0.00675 ( 2) link_ALPHA1-6 : angle 1.97227 ( 6) link_BETA1-4 : bond 0.00473 ( 7) link_BETA1-4 : angle 1.77633 ( 21) link_NAG-ASN : bond 0.00542 ( 6) link_NAG-ASN : angle 3.79273 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 HIS cc_start: 0.8153 (t70) cc_final: 0.7929 (t70) REVERT: A 700 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7141 (tp) REVERT: B 333 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7331 (tt) REVERT: H 36 TRP cc_start: 0.7891 (m100) cc_final: 0.7682 (m100) REVERT: H 81 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7338 (tm-30) REVERT: H 157 TRP cc_start: 0.7060 (m100) cc_final: 0.5729 (m100) REVERT: L 81 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: L 89 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8125 (tp) REVERT: L 138 ASN cc_start: 0.8625 (m-40) cc_final: 0.8397 (m-40) outliers start: 32 outliers final: 19 residues processed: 108 average time/residue: 0.2542 time to fit residues: 38.6685 Evaluate side-chains 94 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 112 optimal weight: 0.0670 chunk 52 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.129432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087338 restraints weight = 61934.563| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.36 r_work: 0.3267 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10993 Z= 0.119 Angle : 0.618 13.548 14965 Z= 0.307 Chirality : 0.045 0.278 1717 Planarity : 0.005 0.127 1926 Dihedral : 9.210 102.009 1836 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.60 % Rotamer: Outliers : 2.64 % Allowed : 21.87 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.30 (0.23), residues: 1353 helix: -0.13 (0.49), residues: 113 sheet: -0.68 (0.21), residues: 525 loop : -1.05 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.012 0.001 TYR H 78 PHE 0.015 0.001 PHE B 93 TRP 0.007 0.001 TRP B 230 HIS 0.002 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00287 (10961) covalent geometry : angle 0.59272 (14884) SS BOND : bond 0.00601 ( 15) SS BOND : angle 1.79667 ( 30) hydrogen bonds : bond 0.03081 ( 374) hydrogen bonds : angle 5.90904 ( 1011) link_ALPHA1-3 : bond 0.01055 ( 2) link_ALPHA1-3 : angle 3.22144 ( 6) link_ALPHA1-6 : bond 0.00657 ( 2) link_ALPHA1-6 : angle 2.12859 ( 6) link_BETA1-4 : bond 0.00448 ( 7) link_BETA1-4 : angle 1.65669 ( 21) link_NAG-ASN : bond 0.00560 ( 6) link_NAG-ASN : angle 3.67294 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 HIS cc_start: 0.8167 (t70) cc_final: 0.7931 (t70) REVERT: B 327 SER cc_start: 0.8199 (m) cc_final: 0.7780 (p) REVERT: H 81 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7185 (tm-30) REVERT: H 157 TRP cc_start: 0.7000 (m100) cc_final: 0.5665 (m100) REVERT: L 81 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: L 138 ASN cc_start: 0.8639 (m-40) cc_final: 0.8411 (m-40) outliers start: 31 outliers final: 24 residues processed: 103 average time/residue: 0.2315 time to fit residues: 34.4995 Evaluate side-chains 98 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.128695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087444 restraints weight = 61114.613| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.24 r_work: 0.3260 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10993 Z= 0.129 Angle : 0.619 13.038 14965 Z= 0.309 Chirality : 0.045 0.280 1717 Planarity : 0.005 0.124 1926 Dihedral : 8.793 102.291 1836 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 2.72 % Allowed : 21.53 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.20 (0.23), residues: 1353 helix: 0.05 (0.50), residues: 113 sheet: -0.64 (0.21), residues: 527 loop : -0.99 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.012 0.001 TYR H 78 PHE 0.015 0.001 PHE B 93 TRP 0.012 0.001 TRP H 36 HIS 0.003 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00310 (10961) covalent geometry : angle 0.59359 (14884) SS BOND : bond 0.00519 ( 15) SS BOND : angle 1.93435 ( 30) hydrogen bonds : bond 0.03041 ( 374) hydrogen bonds : angle 5.80090 ( 1011) link_ALPHA1-3 : bond 0.00972 ( 2) link_ALPHA1-3 : angle 2.98974 ( 6) link_ALPHA1-6 : bond 0.00749 ( 2) link_ALPHA1-6 : angle 2.13729 ( 6) link_BETA1-4 : bond 0.00440 ( 7) link_BETA1-4 : angle 1.61663 ( 21) link_NAG-ASN : bond 0.00569 ( 6) link_NAG-ASN : angle 3.71752 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8880 (tt0) cc_final: 0.8490 (tt0) REVERT: A 700 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7135 (tp) REVERT: B 327 SER cc_start: 0.8266 (m) cc_final: 0.7862 (p) REVERT: H 81 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7255 (tm-30) REVERT: H 157 TRP cc_start: 0.7044 (m100) cc_final: 0.5711 (m100) REVERT: L 81 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: L 89 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8252 (tp) REVERT: L 138 ASN cc_start: 0.8634 (m-40) cc_final: 0.8399 (m-40) outliers start: 32 outliers final: 24 residues processed: 106 average time/residue: 0.2349 time to fit residues: 36.3301 Evaluate side-chains 100 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.126265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084496 restraints weight = 61400.764| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.32 r_work: 0.3198 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10993 Z= 0.182 Angle : 0.640 12.904 14965 Z= 0.321 Chirality : 0.045 0.296 1717 Planarity : 0.005 0.122 1926 Dihedral : 8.326 104.275 1836 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 3.15 % Allowed : 21.87 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.21 (0.23), residues: 1353 helix: 0.16 (0.50), residues: 113 sheet: -0.68 (0.21), residues: 527 loop : -0.98 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.012 0.001 TYR H 50 PHE 0.023 0.001 PHE A 121 TRP 0.023 0.002 TRP H 36 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00415 (10961) covalent geometry : angle 0.61454 (14884) SS BOND : bond 0.00464 ( 15) SS BOND : angle 1.91144 ( 30) hydrogen bonds : bond 0.03263 ( 374) hydrogen bonds : angle 5.74650 ( 1011) link_ALPHA1-3 : bond 0.00862 ( 2) link_ALPHA1-3 : angle 3.07981 ( 6) link_ALPHA1-6 : bond 0.00866 ( 2) link_ALPHA1-6 : angle 2.33439 ( 6) link_BETA1-4 : bond 0.00394 ( 7) link_BETA1-4 : angle 1.55218 ( 21) link_NAG-ASN : bond 0.00586 ( 6) link_NAG-ASN : angle 3.76865 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7957 (ttp) cc_final: 0.7449 (ttm) REVERT: A 700 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7169 (tp) REVERT: B 199 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (p) REVERT: H 81 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7114 (tm-30) REVERT: H 157 TRP cc_start: 0.7154 (m100) cc_final: 0.5823 (m100) REVERT: L 4 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8591 (mtm) REVERT: L 81 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: L 89 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8291 (tp) outliers start: 37 outliers final: 28 residues processed: 111 average time/residue: 0.2219 time to fit residues: 35.8922 Evaluate side-chains 108 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.126063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084326 restraints weight = 61160.595| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.34 r_work: 0.3193 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10993 Z= 0.164 Angle : 0.628 12.814 14965 Z= 0.313 Chirality : 0.045 0.285 1717 Planarity : 0.005 0.121 1926 Dihedral : 7.798 105.640 1836 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 3.40 % Allowed : 21.53 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.14 (0.23), residues: 1353 helix: 0.23 (0.51), residues: 114 sheet: -0.67 (0.22), residues: 522 loop : -0.91 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.016 0.001 TYR H 78 PHE 0.023 0.001 PHE A 121 TRP 0.023 0.002 TRP H 36 HIS 0.004 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00381 (10961) covalent geometry : angle 0.60399 (14884) SS BOND : bond 0.00596 ( 15) SS BOND : angle 1.67213 ( 30) hydrogen bonds : bond 0.03140 ( 374) hydrogen bonds : angle 5.71023 ( 1011) link_ALPHA1-3 : bond 0.00812 ( 2) link_ALPHA1-3 : angle 2.92376 ( 6) link_ALPHA1-6 : bond 0.00938 ( 2) link_ALPHA1-6 : angle 2.51680 ( 6) link_BETA1-4 : bond 0.00398 ( 7) link_BETA1-4 : angle 1.53229 ( 21) link_NAG-ASN : bond 0.00565 ( 6) link_NAG-ASN : angle 3.73422 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8905 (tt0) cc_final: 0.8618 (tt0) REVERT: A 418 MET cc_start: 0.8068 (ttp) cc_final: 0.7540 (ttm) REVERT: A 700 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 199 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 327 SER cc_start: 0.8269 (m) cc_final: 0.7851 (p) REVERT: H 81 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7078 (tm-30) REVERT: H 157 TRP cc_start: 0.7300 (m100) cc_final: 0.5883 (m100) REVERT: L 4 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: L 89 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8307 (tp) outliers start: 40 outliers final: 30 residues processed: 112 average time/residue: 0.2325 time to fit residues: 37.9626 Evaluate side-chains 110 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.083887 restraints weight = 60652.362| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.31 r_work: 0.3192 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10993 Z= 0.153 Angle : 0.617 12.714 14965 Z= 0.308 Chirality : 0.044 0.289 1717 Planarity : 0.005 0.119 1926 Dihedral : 7.162 105.799 1836 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 3.15 % Allowed : 21.87 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.04 (0.23), residues: 1353 helix: 0.35 (0.51), residues: 114 sheet: -0.59 (0.22), residues: 519 loop : -0.87 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.014 0.001 TYR H 78 PHE 0.021 0.001 PHE A 121 TRP 0.031 0.002 TRP H 36 HIS 0.005 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00357 (10961) covalent geometry : angle 0.59384 (14884) SS BOND : bond 0.00407 ( 15) SS BOND : angle 1.66450 ( 30) hydrogen bonds : bond 0.03092 ( 374) hydrogen bonds : angle 5.63089 ( 1011) link_ALPHA1-3 : bond 0.00868 ( 2) link_ALPHA1-3 : angle 2.68678 ( 6) link_ALPHA1-6 : bond 0.01251 ( 2) link_ALPHA1-6 : angle 2.13978 ( 6) link_BETA1-4 : bond 0.00341 ( 7) link_BETA1-4 : angle 1.51815 ( 21) link_NAG-ASN : bond 0.00565 ( 6) link_NAG-ASN : angle 3.70245 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8904 (tt0) cc_final: 0.8643 (tt0) REVERT: A 418 MET cc_start: 0.8075 (ttp) cc_final: 0.7536 (ttm) REVERT: B 199 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 327 SER cc_start: 0.8433 (m) cc_final: 0.7957 (p) REVERT: H 81 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7144 (tm-30) REVERT: H 157 TRP cc_start: 0.7304 (m100) cc_final: 0.5930 (m100) REVERT: L 4 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8718 (mtm) REVERT: L 89 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8289 (tp) REVERT: L 175 MET cc_start: 0.3938 (tmm) cc_final: 0.3732 (tmm) outliers start: 37 outliers final: 28 residues processed: 106 average time/residue: 0.2181 time to fit residues: 34.1150 Evaluate side-chains 103 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN A 741 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.124491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082721 restraints weight = 61107.505| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.30 r_work: 0.3169 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10993 Z= 0.192 Angle : 0.632 12.935 14965 Z= 0.318 Chirality : 0.045 0.292 1717 Planarity : 0.005 0.118 1926 Dihedral : 7.073 105.934 1836 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 3.40 % Allowed : 21.79 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.05 (0.23), residues: 1353 helix: 0.34 (0.52), residues: 114 sheet: -0.58 (0.22), residues: 521 loop : -0.88 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.014 0.001 TYR H 78 PHE 0.025 0.001 PHE A 121 TRP 0.036 0.002 TRP H 36 HIS 0.005 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00441 (10961) covalent geometry : angle 0.60838 (14884) SS BOND : bond 0.00456 ( 15) SS BOND : angle 1.67153 ( 30) hydrogen bonds : bond 0.03207 ( 374) hydrogen bonds : angle 5.64598 ( 1011) link_ALPHA1-3 : bond 0.00849 ( 2) link_ALPHA1-3 : angle 2.80885 ( 6) link_ALPHA1-6 : bond 0.01016 ( 2) link_ALPHA1-6 : angle 1.94473 ( 6) link_BETA1-4 : bond 0.00338 ( 7) link_BETA1-4 : angle 1.57914 ( 21) link_NAG-ASN : bond 0.00636 ( 6) link_NAG-ASN : angle 3.78762 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8942 (tt0) cc_final: 0.8687 (tt0) REVERT: A 418 MET cc_start: 0.8086 (ttp) cc_final: 0.7576 (ttm) REVERT: B 199 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8493 (p) REVERT: B 327 SER cc_start: 0.8449 (m) cc_final: 0.7977 (p) REVERT: H 16 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6487 (pp30) REVERT: H 81 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7134 (tm-30) REVERT: H 157 TRP cc_start: 0.7305 (m100) cc_final: 0.5911 (m100) REVERT: L 4 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8750 (mtm) REVERT: L 89 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8273 (tp) REVERT: L 175 MET cc_start: 0.4116 (tmm) cc_final: 0.3782 (tmm) outliers start: 40 outliers final: 31 residues processed: 110 average time/residue: 0.2234 time to fit residues: 36.0219 Evaluate side-chains 109 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 111 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082596 restraints weight = 61390.877| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.30 r_work: 0.3166 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10993 Z= 0.187 Angle : 0.633 12.878 14965 Z= 0.319 Chirality : 0.045 0.291 1717 Planarity : 0.005 0.118 1926 Dihedral : 7.083 106.003 1836 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 3.23 % Allowed : 22.04 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.06 (0.23), residues: 1353 helix: 0.31 (0.51), residues: 114 sheet: -0.58 (0.22), residues: 519 loop : -0.89 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.014 0.001 TYR H 78 PHE 0.024 0.001 PHE A 121 TRP 0.038 0.002 TRP H 36 HIS 0.004 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00433 (10961) covalent geometry : angle 0.60990 (14884) SS BOND : bond 0.00427 ( 15) SS BOND : angle 1.65277 ( 30) hydrogen bonds : bond 0.03197 ( 374) hydrogen bonds : angle 5.66281 ( 1011) link_ALPHA1-3 : bond 0.00815 ( 2) link_ALPHA1-3 : angle 2.65253 ( 6) link_ALPHA1-6 : bond 0.00950 ( 2) link_ALPHA1-6 : angle 1.91212 ( 6) link_BETA1-4 : bond 0.00322 ( 7) link_BETA1-4 : angle 1.57803 ( 21) link_NAG-ASN : bond 0.00618 ( 6) link_NAG-ASN : angle 3.75430 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 578 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue THR 692 is missing expected H atoms. Skipping. Residue THR 694 is missing expected H atoms. Skipping. Residue THR 697 is missing expected H atoms. Skipping. Residue THR 724 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8920 (tt0) cc_final: 0.8662 (tt0) REVERT: A 418 MET cc_start: 0.8093 (ttp) cc_final: 0.7578 (ttm) REVERT: B 199 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 327 SER cc_start: 0.8463 (m) cc_final: 0.7988 (p) REVERT: H 81 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7046 (tm-30) REVERT: H 157 TRP cc_start: 0.7323 (m100) cc_final: 0.5928 (m100) REVERT: L 4 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8745 (mtm) REVERT: L 89 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8293 (tp) REVERT: L 175 MET cc_start: 0.4174 (tmm) cc_final: 0.3894 (tmm) outliers start: 38 outliers final: 33 residues processed: 109 average time/residue: 0.2163 time to fit residues: 35.1294 Evaluate side-chains 110 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081990 restraints weight = 61358.926| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.39 r_work: 0.3162 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 10993 Z= 0.228 Angle : 0.878 59.142 14965 Z= 0.501 Chirality : 0.045 0.292 1717 Planarity : 0.005 0.118 1926 Dihedral : 7.079 105.927 1836 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 3.15 % Allowed : 22.47 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -1.06 (0.23), residues: 1353 helix: 0.32 (0.51), residues: 114 sheet: -0.58 (0.22), residues: 519 loop : -0.89 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.013 0.001 TYR H 78 PHE 0.023 0.001 PHE A 121 TRP 0.029 0.002 TRP H 36 HIS 0.004 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00503 (10961) covalent geometry : angle 0.86341 (14884) SS BOND : bond 0.00468 ( 15) SS BOND : angle 1.66927 ( 30) hydrogen bonds : bond 0.03202 ( 374) hydrogen bonds : angle 5.66162 ( 1011) link_ALPHA1-3 : bond 0.00724 ( 2) link_ALPHA1-3 : angle 2.60277 ( 6) link_ALPHA1-6 : bond 0.00951 ( 2) link_ALPHA1-6 : angle 1.92002 ( 6) link_BETA1-4 : bond 0.00320 ( 7) link_BETA1-4 : angle 1.57928 ( 21) link_NAG-ASN : bond 0.00622 ( 6) link_NAG-ASN : angle 3.75561 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6279.30 seconds wall clock time: 107 minutes 16.62 seconds (6436.62 seconds total)