Starting phenix.real_space_refine on Thu Aug 6 23:54:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ytc_73457/08_2026/9ytc_73457.map" } resolution = 2.68 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= 0.008 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: 5 Type Number sf(0) Gaussians S 33 5.16 5 C 5582 2.51 5 N 1487 2.21 5 O 1751 1.98 5 H 8505 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17358 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4208 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "D" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3372 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3193 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3306 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3227 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.96, per 1000 atoms: 0.17 Number of scatterers: 17358 At special positions: 0 Unit cell: (92.71, 104.39, 167.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 O 1751 8.00 N 1487 7.00 C 5582 6.00 H 8505 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 331 " " NAG T 1 " - " ASN A 343 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 476.7 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 27 sheets defined 10.8% alpha, 44.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.712A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.523A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.276A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.024A pdb=" N THR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.605A pdb=" N GLY D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 120 through 127 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.715A pdb=" N HIS E 188 " --> pdb=" O TYR E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASN F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 134 through 138 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.522A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.030A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.975A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.543A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.569A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.184A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.184A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 154 Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.894A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.373A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.797A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 154 removed outlier: 4.403A pdb=" N TRP E 147 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.492A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.872A pdb=" N VAL F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.086A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.086A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 157 through 160 removed outlier: 4.364A pdb=" N TYR F 200 " --> pdb=" O VAL F 217 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.813A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.992A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 153 through 154 400 hydrogen bonds defined for protein. 960 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: 3.70 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8503 1.04 - 1.24: 1253 1.24 - 1.44: 2788 1.44 - 1.65: 4990 1.65 - 1.85: 39 Bond restraints: 17573 Sorted by residual: bond pdb=" CB GLU E 142 " pdb=" CG GLU E 142 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N VAL A 320 " pdb=" H VAL A 320 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 1.808 1.848 -0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.24e+00 ... (remaining 17568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 30744 1.41 - 2.82: 743 2.82 - 4.23: 106 4.23 - 5.64: 9 5.64 - 7.05: 3 Bond angle restraints: 31605 Sorted by residual: angle pdb=" CB GLU E 142 " pdb=" CG GLU E 142 " pdb=" CD GLU E 142 " ideal model delta sigma weight residual 112.60 119.65 -7.05 1.70e+00 3.46e-01 1.72e+01 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 111.91 108.98 2.93 8.90e-01 1.26e+00 1.08e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.25 -6.85 2.30e+00 1.89e-01 8.88e+00 angle pdb=" CA GLU E 142 " pdb=" CB GLU E 142 " pdb=" CG GLU E 142 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.16e+00 angle pdb=" N SER G 30 " pdb=" CA SER G 30 " pdb=" C SER G 30 " ideal model delta sigma weight residual 110.80 116.41 -5.61 2.13e+00 2.20e-01 6.94e+00 ... (remaining 31600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7666 17.63 - 35.27: 558 35.27 - 52.90: 209 52.90 - 70.53: 76 70.53 - 88.16: 10 Dihedral angle restraints: 8519 sinusoidal: 4581 harmonic: 3938 Sorted by residual: dihedral pdb=" CA TYR G 91 " pdb=" C TYR G 91 " pdb=" N ASP G 92 " pdb=" CA ASP G 92 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 47.68 45.32 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS F 146 " pdb=" SG CYS F 146 " pdb=" SG CYS F 202 " pdb=" CB CYS F 202 " ideal model delta sinusoidal sigma weight residual 93.00 58.23 34.77 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 752 0.028 - 0.056: 442 0.056 - 0.084: 69 0.084 - 0.113: 86 0.113 - 0.141: 35 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE E 48 " pdb=" N ILE E 48 " pdb=" C ILE E 48 " pdb=" CB ILE E 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL F 93 " pdb=" N VAL F 93 " pdb=" C VAL F 93 " pdb=" CB VAL F 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1381 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 142 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C GLU E 142 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU E 142 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA E 143 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 141 " 0.176 9.50e-02 1.11e+02 5.88e-02 4.01e+00 pdb=" NE ARG E 141 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 141 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 141 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 141 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 141 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG E 141 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 141 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG E 141 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 577 " 0.125 9.50e-02 1.11e+02 4.18e-02 2.16e+00 pdb=" NE ARG A 577 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 577 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 577 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 577 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 577 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 577 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 577 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 577 " 0.000 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 912 2.18 - 2.78: 34455 2.78 - 3.39: 47824 3.39 - 3.99: 66533 3.99 - 4.60: 99193 Nonbonded interactions: 248917 Sorted by model distance: nonbonded pdb="HH12 ARG E 61 " pdb=" OD2 ASP E 82 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU E 186 " pdb=" H GLU E 186 " model vdw 1.597 2.450 nonbonded pdb=" O ASP A 574 " pdb=" H ILE A 587 " model vdw 1.628 2.450 nonbonded pdb=" H ARG F 87 " pdb=" OD2 ASP F 90 " model vdw 1.629 2.450 nonbonded pdb="HH22 ARG A 454 " pdb=" O SER A 469 " model vdw 1.630 2.450 ... (remaining 248912 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' and (resid 1 through 18 or resid 20 through 23 or resid 25 through 30 \ or resid 34 through 50 or resid 52 through 52A or resid 54 through 55 or resid \ 57 through 58 or resid 60 through 61 or resid 63 through 64 or resid 66 through \ 75 or resid 77 through 80 or resid 82 through 82C or resid 84 through 94 or resi \ d 96 or resid 100C through 100D or resid 100F through 126 or resid 128 or resid \ 130 through 132 or resid 135 through 191 or resid 193 through 194 or resid 196 t \ hrough 198 or (resid 200 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA o \ r name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 201 throug \ h 209 or resid 211 through 212 or resid 214)) selection = (chain 'F' and (resid 1 through 18 or resid 20 through 23 or resid 25 through 30 \ or resid 34 through 50 or resid 52 through 53 or resid 55 through 56 or resid 5 \ 8 through 59 or resid 61 through 62 or resid 64 through 65 or resid 67 through 7 \ 6 or resid 78 through 81 or resid 83 through 86 or resid 88 through 99 or resid \ 102 through 103 or resid 105 through 132 or resid 134 or resid 136 through 138 o \ r resid 141 through 197 or resid 199 through 200 or resid 202 through 204 or res \ id 206 through 215 or resid 217 through 218 or resid 220)) } ncs_group { reference = (chain 'E' and (resid 1 through 30 or resid 32 through 38 or resid 40 through 41 \ or resid 43 through 55 or resid 57 through 62 or resid 64 through 83 or resid 8 \ 5 through 89 or resid 91 through 92 or resid 94 or resid 96 through 212)) selection = (chain 'G' and (resid 1 through 30 or resid 32 through 38 or resid 40 through 41 \ or resid 43 through 55 or resid 57 through 62 or resid 64 through 83 or resid 8 \ 5 through 89 or resid 91 through 92 or resid 94 or resid 97 through 213)) } 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: 9.020 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: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:5.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9084 Z= 0.141 Angle : 0.607 7.047 12382 Z= 0.331 Chirality : 0.043 0.141 1384 Planarity : 0.004 0.077 1589 Dihedral : 13.671 88.163 3295 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.70 % Favored : 95.12 % Rotamer: Outliers : 0.20 % Allowed : 13.10 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1127 helix: -2.89 (0.55), residues: 50 sheet: 0.51 (0.23), residues: 488 loop : 0.03 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 577 TYR 0.014 0.001 TYR G 140 PHE 0.007 0.001 PHE D 100C TRP 0.012 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9068) covalent geometry : angle 0.60268 / 0.33 (12346) SS BOND : bond 0.00325 / 0.16 ( 12) SS BOND : angle 1.04770 / 0.54 ( 24) hydrogen bonds : bond 0.20441 / 13.34 ( 344) hydrogen bonds : angle 9.46163 / 6.51 ( 960) link_BETA1-4 : bond 0.00881 / 0.46 ( 1) link_BETA1-4 : angle 2.18987 / 1.13 ( 3) link_BETA1-6 : bond 0.01507 / 0.79 ( 1) link_BETA1-6 : angle 1.29280 / 0.72 ( 3) link_NAG-ASN : bond 0.00166 / 0.09 ( 2) link_NAG-ASN : angle 2.21888 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 1.0430 time to fit residues: 70.9562 Evaluate side-chains 60 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 61 GLN D 171 GLN F 210 ASN G 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.053344 restraints weight = 49904.872| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.52 r_work: 0.2645 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9084 Z= 0.210 Angle : 0.605 8.141 12382 Z= 0.315 Chirality : 0.046 0.164 1384 Planarity : 0.004 0.054 1589 Dihedral : 5.671 56.940 1314 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.06 % Favored : 94.76 % Rotamer: Outliers : 0.81 % Allowed : 12.49 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1127 helix: -2.96 (0.53), residues: 50 sheet: 0.62 (0.23), residues: 484 loop : -0.14 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 141 TYR 0.015 0.001 TYR E 91 PHE 0.008 0.001 PHE A 429 TRP 0.014 0.001 TRP F 50 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 9068) covalent geometry : angle 0.59953 / 0.31 (12346) SS BOND : bond 0.00373 / 0.23 ( 12) SS BOND : angle 1.39085 / 0.82 ( 24) hydrogen bonds : bond 0.04386 / 2.82 ( 344) hydrogen bonds : angle 6.90551 / 4.78 ( 960) link_BETA1-4 : bond 0.00096 / 0.05 ( 1) link_BETA1-4 : angle 1.39249 / 0.70 ( 3) link_BETA1-6 : bond 0.00978 / 0.51 ( 1) link_BETA1-6 : angle 2.15643 / 1.18 ( 3) link_NAG-ASN : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : angle 2.09597 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8245 (pt0) cc_final: 0.7397 (pm20) REVERT: D 10 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8158 (mt-10) REVERT: D 210 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7983 (ttt-90) REVERT: E 81 GLU cc_start: 0.8671 (pm20) cc_final: 0.8172 (pm20) REVERT: F 1 GLN cc_start: 0.7396 (pm20) cc_final: 0.7171 (pm20) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 1.1145 time to fit residues: 86.6681 Evaluate side-chains 63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.053836 restraints weight = 50256.637| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.51 r_work: 0.2655 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9084 Z= 0.168 Angle : 0.574 8.154 12382 Z= 0.294 Chirality : 0.045 0.156 1384 Planarity : 0.004 0.068 1589 Dihedral : 5.547 56.421 1312 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.06 % Favored : 94.76 % Rotamer: Outliers : 0.61 % Allowed : 13.30 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1127 helix: -2.96 (0.54), residues: 50 sheet: 0.48 (0.22), residues: 491 loop : -0.18 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE A 429 TRP 0.011 0.001 TRP F 50 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9068) covalent geometry : angle 0.56881 / 0.29 (12346) SS BOND : bond 0.00374 / 0.26 ( 12) SS BOND : angle 1.37983 / 0.81 ( 24) hydrogen bonds : bond 0.03634 / 2.37 ( 344) hydrogen bonds : angle 6.27803 / 4.37 ( 960) link_BETA1-4 : bond 0.00278 / 0.15 ( 1) link_BETA1-4 : angle 1.17533 / 0.60 ( 3) link_BETA1-6 : bond 0.00788 / 0.41 ( 1) link_BETA1-6 : angle 1.75054 / 0.95 ( 3) link_NAG-ASN : bond 0.00019 / 0.01 ( 2) link_NAG-ASN : angle 1.87196 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8268 (pt0) cc_final: 0.7396 (pm20) REVERT: D 10 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8129 (mt-10) REVERT: E 81 GLU cc_start: 0.8524 (pm20) cc_final: 0.8113 (pm20) outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 1.1193 time to fit residues: 89.4971 Evaluate side-chains 63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain E residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.054156 restraints weight = 50044.972| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.52 r_work: 0.2664 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9084 Z= 0.147 Angle : 0.562 7.791 12382 Z= 0.288 Chirality : 0.045 0.156 1384 Planarity : 0.004 0.062 1589 Dihedral : 5.473 56.452 1312 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.97 % Favored : 94.85 % Rotamer: Outliers : 0.81 % Allowed : 14.11 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1127 helix: -2.81 (0.59), residues: 50 sheet: 0.48 (0.22), residues: 491 loop : -0.20 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE G 73 TRP 0.011 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9068) covalent geometry : angle 0.55678 / 0.29 (12346) SS BOND : bond 0.00397 / 0.37 ( 12) SS BOND : angle 1.43051 / 0.81 ( 24) hydrogen bonds : bond 0.03182 / 2.09 ( 344) hydrogen bonds : angle 6.02722 / 4.20 ( 960) link_BETA1-4 : bond 0.00284 / 0.15 ( 1) link_BETA1-4 : angle 1.12840 / 0.57 ( 3) link_BETA1-6 : bond 0.00910 / 0.48 ( 1) link_BETA1-6 : angle 1.79596 / 0.97 ( 3) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 1.76701 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8299 (pt0) cc_final: 0.7427 (pm20) REVERT: D 10 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8088 (mt-10) REVERT: D 19 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8857 (tppt) REVERT: E 81 GLU cc_start: 0.8437 (pm20) cc_final: 0.8026 (pm20) REVERT: E 210 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8129 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 1.1191 time to fit residues: 84.7360 Evaluate side-chains 67 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain E residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053484 restraints weight = 49753.495| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.50 r_work: 0.2647 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9084 Z= 0.190 Angle : 0.571 7.890 12382 Z= 0.292 Chirality : 0.045 0.159 1384 Planarity : 0.004 0.069 1589 Dihedral : 5.542 56.921 1312 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.91 % Allowed : 14.21 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1127 helix: -2.79 (0.59), residues: 50 sheet: 0.48 (0.22), residues: 490 loop : -0.23 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 141 TYR 0.014 0.001 TYR E 91 PHE 0.007 0.001 PHE A 429 TRP 0.012 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 9068) covalent geometry : angle 0.56574 / 0.29 (12346) SS BOND : bond 0.00344 / 0.21 ( 12) SS BOND : angle 1.38933 / 0.81 ( 24) hydrogen bonds : bond 0.03168 / 2.08 ( 344) hydrogen bonds : angle 5.91398 / 4.12 ( 960) link_BETA1-4 : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : angle 1.20589 / 0.62 ( 3) link_BETA1-6 : bond 0.00820 / 0.43 ( 1) link_BETA1-6 : angle 1.96977 / 1.06 ( 3) link_NAG-ASN : bond 0.00090 / 0.04 ( 2) link_NAG-ASN : angle 1.84209 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.506 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: A 324 GLU cc_start: 0.8333 (pt0) cc_final: 0.7458 (pm20) REVERT: D 10 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8180 (mt-10) REVERT: E 81 GLU cc_start: 0.8439 (pm20) cc_final: 0.8037 (pm20) REVERT: E 210 ARG cc_start: 0.8681 (tmm-80) cc_final: 0.8166 (tmm-80) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 1.1056 time to fit residues: 86.1948 Evaluate side-chains 66 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056067 restraints weight = 52277.752| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.55 r_work: 0.2718 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9084 Z= 0.159 Angle : 0.561 7.721 12382 Z= 0.286 Chirality : 0.044 0.158 1384 Planarity : 0.004 0.060 1589 Dihedral : 5.526 56.860 1312 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 1.32 % Allowed : 14.11 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1127 helix: -2.75 (0.60), residues: 50 sheet: 0.49 (0.22), residues: 489 loop : -0.25 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE A 429 TRP 0.011 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9068) covalent geometry : angle 0.55577 / 0.28 (12346) SS BOND : bond 0.00324 / 0.19 ( 12) SS BOND : angle 1.48926 / 0.90 ( 24) hydrogen bonds : bond 0.03010 / 1.98 ( 344) hydrogen bonds : angle 5.77869 / 4.03 ( 960) link_BETA1-4 : bond 0.00175 / 0.09 ( 1) link_BETA1-4 : angle 1.15028 / 0.60 ( 3) link_BETA1-6 : bond 0.00884 / 0.47 ( 1) link_BETA1-6 : angle 1.98916 / 1.06 ( 3) link_NAG-ASN : bond 0.00021 / 0.01 ( 2) link_NAG-ASN : angle 1.74916 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.500 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: A 324 GLU cc_start: 0.8297 (pt0) cc_final: 0.7452 (pm20) REVERT: D 10 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8055 (mt-10) REVERT: D 210 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7711 (tpt90) REVERT: E 81 GLU cc_start: 0.8325 (pm20) cc_final: 0.7924 (pm20) REVERT: E 210 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8127 (tmm-80) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 1.0666 time to fit residues: 85.4130 Evaluate side-chains 70 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 24 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056406 restraints weight = 52272.826| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.56 r_work: 0.2731 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9084 Z= 0.145 Angle : 0.558 7.540 12382 Z= 0.284 Chirality : 0.044 0.157 1384 Planarity : 0.004 0.063 1589 Dihedral : 5.481 56.751 1312 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 0.91 % Allowed : 14.82 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1127 helix: -2.72 (0.59), residues: 50 sheet: 0.48 (0.22), residues: 489 loop : -0.22 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.007 0.001 PHE A 565 TRP 0.011 0.001 TRP F 50 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9068) covalent geometry : angle 0.55295 / 0.28 (12346) SS BOND : bond 0.00316 / 0.19 ( 12) SS BOND : angle 1.34212 / 0.80 ( 24) hydrogen bonds : bond 0.02911 / 1.92 ( 344) hydrogen bonds : angle 5.65258 / 3.94 ( 960) link_BETA1-4 : bond 0.00200 / 0.11 ( 1) link_BETA1-4 : angle 1.12635 / 0.58 ( 3) link_BETA1-6 : bond 0.00876 / 0.46 ( 1) link_BETA1-6 : angle 1.91728 / 1.02 ( 3) link_NAG-ASN : bond 0.00055 / 0.03 ( 2) link_NAG-ASN : angle 1.70163 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.393 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: A 324 GLU cc_start: 0.8305 (pt0) cc_final: 0.7471 (pm20) REVERT: A 577 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: D 10 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8059 (mt-10) REVERT: E 81 GLU cc_start: 0.8301 (pm20) cc_final: 0.7908 (pm20) REVERT: E 194 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7950 (pt0) REVERT: E 210 ARG cc_start: 0.8692 (tmm-80) cc_final: 0.8137 (tmm-80) REVERT: F 43 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7386 (mp10) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 1.0907 time to fit residues: 84.9184 Evaluate side-chains 70 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 43 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 152 ASN G 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.056272 restraints weight = 52474.798| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.56 r_work: 0.2727 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9084 Z= 0.156 Angle : 0.558 7.419 12382 Z= 0.284 Chirality : 0.044 0.158 1384 Planarity : 0.004 0.065 1589 Dihedral : 5.506 56.862 1312 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 1.02 % Allowed : 14.52 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1127 helix: -2.71 (0.59), residues: 50 sheet: 0.49 (0.22), residues: 489 loop : -0.21 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE A 429 TRP 0.012 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 9068) covalent geometry : angle 0.55363 / 0.28 (12346) SS BOND : bond 0.00317 / 0.19 ( 12) SS BOND : angle 1.29157 / 0.77 ( 24) hydrogen bonds : bond 0.02905 / 1.91 ( 344) hydrogen bonds : angle 5.59864 / 3.90 ( 960) link_BETA1-4 : bond 0.00108 / 0.06 ( 1) link_BETA1-4 : angle 1.16789 / 0.61 ( 3) link_BETA1-6 : bond 0.00995 / 0.52 ( 1) link_BETA1-6 : angle 2.05248 / 1.09 ( 3) link_NAG-ASN : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : angle 1.70734 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8305 (pt0) cc_final: 0.7479 (pm20) REVERT: A 577 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7586 (ttm-80) REVERT: D 10 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 72 ASP cc_start: 0.8052 (t0) cc_final: 0.7789 (t0) REVERT: E 81 GLU cc_start: 0.8271 (pm20) cc_final: 0.7893 (pm20) REVERT: E 194 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7981 (pt0) REVERT: E 210 ARG cc_start: 0.8684 (tmm-80) cc_final: 0.8129 (tmm-80) REVERT: F 43 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7351 (mp10) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 1.0557 time to fit residues: 83.2854 Evaluate side-chains 69 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain G residue 210 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 152 ASN G 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056760 restraints weight = 52240.219| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.55 r_work: 0.2733 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9084 Z= 0.133 Angle : 0.560 7.172 12382 Z= 0.285 Chirality : 0.044 0.157 1384 Planarity : 0.004 0.065 1589 Dihedral : 5.485 56.831 1312 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 1.02 % Allowed : 14.31 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1127 helix: -2.72 (0.59), residues: 50 sheet: 0.51 (0.22), residues: 488 loop : -0.21 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 141 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE D 100C TRP 0.011 0.001 TRP F 50 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9068) covalent geometry : angle 0.55584 / 0.28 (12346) SS BOND : bond 0.00304 / 0.18 ( 12) SS BOND : angle 1.22159 / 0.72 ( 24) hydrogen bonds : bond 0.02831 / 1.87 ( 344) hydrogen bonds : angle 5.53551 / 3.86 ( 960) link_BETA1-4 : bond 0.00170 / 0.09 ( 1) link_BETA1-4 : angle 1.11190 / 0.58 ( 3) link_BETA1-6 : bond 0.00894 / 0.47 ( 1) link_BETA1-6 : angle 1.92283 / 1.02 ( 3) link_NAG-ASN : bond 0.00092 / 0.04 ( 2) link_NAG-ASN : angle 1.62369 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.526 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: A 324 GLU cc_start: 0.8318 (pt0) cc_final: 0.7484 (pm20) REVERT: A 577 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: D 10 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 72 ASP cc_start: 0.8036 (t0) cc_final: 0.7772 (t0) REVERT: D 210 ARG cc_start: 0.8532 (mmt180) cc_final: 0.8271 (tpt90) REVERT: E 81 GLU cc_start: 0.8259 (pm20) cc_final: 0.7884 (pm20) REVERT: E 194 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7994 (pt0) REVERT: E 210 ARG cc_start: 0.8681 (tmm-80) cc_final: 0.8158 (tmm-80) REVERT: F 43 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7378 (mp10) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 1.0093 time to fit residues: 76.2558 Evaluate side-chains 68 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain G residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055715 restraints weight = 51249.533| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.63 r_work: 0.2742 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9084 Z= 0.127 Angle : 0.554 6.885 12382 Z= 0.282 Chirality : 0.044 0.155 1384 Planarity : 0.003 0.033 1589 Dihedral : 5.450 56.720 1312 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 1.02 % Allowed : 14.52 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1127 helix: -2.73 (0.58), residues: 50 sheet: 0.48 (0.22), residues: 494 loop : -0.20 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.013 0.001 TYR E 91 PHE 0.006 0.001 PHE G 73 TRP 0.011 0.001 TRP F 50 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9068) covalent geometry : angle 0.54999 / 0.28 (12346) SS BOND : bond 0.00295 / 0.18 ( 12) SS BOND : angle 1.17174 / 0.69 ( 24) hydrogen bonds : bond 0.02782 / 1.82 ( 344) hydrogen bonds : angle 5.44061 / 3.80 ( 960) link_BETA1-4 : bond 0.00223 / 0.12 ( 1) link_BETA1-4 : angle 1.12902 / 0.59 ( 3) link_BETA1-6 : bond 0.00890 / 0.47 ( 1) link_BETA1-6 : angle 1.89218 / 1.00 ( 3) link_NAG-ASN : bond 0.00109 / 0.05 ( 2) link_NAG-ASN : angle 1.56515 / 0.72 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.492 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: A 324 GLU cc_start: 0.8310 (pt0) cc_final: 0.7522 (pm20) REVERT: A 577 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7535 (ttm-80) REVERT: D 10 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 72 ASP cc_start: 0.7914 (t0) cc_final: 0.7629 (t0) REVERT: D 210 ARG cc_start: 0.8614 (mmt180) cc_final: 0.8219 (tpt90) REVERT: E 81 GLU cc_start: 0.8194 (pm20) cc_final: 0.7850 (pm20) REVERT: E 154 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8601 (mm110) REVERT: E 210 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8133 (tmm-80) REVERT: F 43 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7302 (mp10) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 1.1071 time to fit residues: 85.8373 Evaluate side-chains 71 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain G residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055577 restraints weight = 51576.615| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.62 r_work: 0.2741 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9084 Z= 0.139 Angle : 0.564 7.190 12382 Z= 0.289 Chirality : 0.044 0.156 1384 Planarity : 0.004 0.056 1589 Dihedral : 5.503 56.750 1312 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 0.81 % Allowed : 14.62 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1127 helix: -2.79 (0.59), residues: 50 sheet: 0.47 (0.22), residues: 493 loop : -0.21 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 141 TYR 0.028 0.001 TYR E 185 PHE 0.006 0.001 PHE G 209 TRP 0.011 0.001 TRP F 50 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9068) covalent geometry : angle 0.56054 / 0.29 (12346) SS BOND : bond 0.00295 / 0.18 ( 12) SS BOND : angle 1.17546 / 0.70 ( 24) hydrogen bonds : bond 0.02833 / 1.85 ( 344) hydrogen bonds : angle 5.45292 / 3.82 ( 960) link_BETA1-4 : bond 0.00242 / 0.13 ( 1) link_BETA1-4 : angle 1.17366 / 0.62 ( 3) link_BETA1-6 : bond 0.00850 / 0.45 ( 1) link_BETA1-6 : angle 1.88303 / 1.00 ( 3) link_NAG-ASN : bond 0.00068 / 0.03 ( 2) link_NAG-ASN : angle 1.58601 / 0.73 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6154.64 seconds wall clock time: 104 minutes 50.23 seconds (6290.23 seconds total)