Starting phenix.real_space_refine on Wed Mar 4 08:41:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ri4_24473/03_2026/7ri4_24473.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7713 2.51 5 N 2097 2.21 5 O 2402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12248 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 434 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 6189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6189 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 752} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2733 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1760 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 2.72, per 1000 atoms: 0.22 Number of scatterers: 12248 At special positions: 0 Unit cell: (108, 143.64, 127.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2402 8.00 N 2097 7.00 C 7713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G1226 " - pdb=" SG CYS A 806 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 792.9 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 19.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.702A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.882A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 4.159A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 removed outlier: 4.019A pdb=" N PHE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.061A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.811A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.516A pdb=" N LYS A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.526A pdb=" N VAL A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.994A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.562A pdb=" N GLU A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 651' Processing helix chain 'A' and resid 655 through 660 removed outlier: 3.772A pdb=" N THR A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.717A pdb=" N ALA A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.595A pdb=" N ARG B 243 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 244 " --> pdb=" O ILE B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'D' and resid 33 through 44 removed outlier: 3.894A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 4.377A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 82 removed outlier: 4.064A pdb=" N GLN D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.803A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.562A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 3.883A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.668A pdb=" N THR D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.618A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 214 through 223 removed outlier: 4.020A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 4.011A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.574A pdb=" N LYS E 45 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.520A pdb=" N TYR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.323A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.846A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 156 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.836A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 247 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 7.374A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.901A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA8, first strand: chain 'A' and resid 461 through 462 removed outlier: 4.284A pdb=" N TYR A 468 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 485 through 492 removed outlier: 3.985A pdb=" N ALA A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 576 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 592 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 564 through 569 removed outlier: 3.580A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 576 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 592 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 49 removed outlier: 7.007A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.549A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 118 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AB6, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.596A pdb=" N ASN B 287 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 299 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B 289 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 297 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.736A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.736A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2821 1.46 - 1.58: 5514 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 12509 Sorted by residual: bond pdb=" C PRO D 31 " pdb=" N PRO D 32 " ideal model delta sigma weight residual 1.326 1.366 -0.040 1.44e-02 4.82e+03 7.69e+00 bond pdb=" CA GLY C 77 " pdb=" C GLY C 77 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.47e+00 bond pdb=" C LEU D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.24e+00 bond pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.76e+00 bond pdb=" C ILE C 67 " pdb=" N PRO C 68 " ideal model delta sigma weight residual 1.331 1.347 -0.015 1.21e-02 6.83e+03 1.61e+00 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 16826 2.84 - 5.69: 162 5.69 - 8.53: 14 8.53 - 11.38: 0 11.38 - 14.22: 1 Bond angle restraints: 17003 Sorted by residual: angle pdb=" N TYR A 548 " pdb=" CA TYR A 548 " pdb=" C TYR A 548 " ideal model delta sigma weight residual 113.18 107.37 5.81 1.33e+00 5.65e-01 1.91e+01 angle pdb=" N ILE B 92 " pdb=" CA ILE B 92 " pdb=" C ILE B 92 " ideal model delta sigma weight residual 112.12 108.49 3.63 8.40e-01 1.42e+00 1.86e+01 angle pdb=" N ASP B 384 " pdb=" CA ASP B 384 " pdb=" C ASP B 384 " ideal model delta sigma weight residual 114.56 109.15 5.41 1.27e+00 6.20e-01 1.81e+01 angle pdb=" N ASN G1290 " pdb=" CA ASN G1290 " pdb=" C ASN G1290 " ideal model delta sigma weight residual 108.23 113.96 -5.73 1.38e+00 5.25e-01 1.72e+01 angle pdb=" CA LEU G1259 " pdb=" CB LEU G1259 " pdb=" CG LEU G1259 " ideal model delta sigma weight residual 116.30 130.52 -14.22 3.50e+00 8.16e-02 1.65e+01 ... (remaining 16998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6359 17.97 - 35.95: 794 35.95 - 53.92: 187 53.92 - 71.90: 29 71.90 - 89.87: 20 Dihedral angle restraints: 7389 sinusoidal: 2855 harmonic: 4534 Sorted by residual: dihedral pdb=" CA ASN D 30 " pdb=" C ASN D 30 " pdb=" N PRO D 31 " pdb=" CA PRO D 31 " ideal model delta harmonic sigma weight residual 180.00 140.15 39.85 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA PRO D 31 " pdb=" C PRO D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta harmonic sigma weight residual -180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA ASP G1289 " pdb=" C ASP G1289 " pdb=" N ASN G1290 " pdb=" CA ASN G1290 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1378 0.044 - 0.088: 370 0.088 - 0.132: 108 0.132 - 0.176: 4 0.176 - 0.220: 2 Chirality restraints: 1862 Sorted by residual: chirality pdb=" CG LEU G1259 " pdb=" CB LEU G1259 " pdb=" CD1 LEU G1259 " pdb=" CD2 LEU G1259 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" C PRO D 86 " pdb=" CB PRO D 86 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" C PRO A 602 " pdb=" CB PRO A 602 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1859 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 30 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 31 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 675 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 676 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A 541 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.023 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2132 2.77 - 3.30: 11579 3.30 - 3.84: 18768 3.84 - 4.37: 21159 4.37 - 4.90: 37273 Nonbonded interactions: 90911 Sorted by model distance: nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 70 " model vdw 2.238 3.040 nonbonded pdb=" ND2 ASN A 102 " pdb=" O VAL A 105 " model vdw 2.250 3.120 nonbonded pdb=" N ALA B 260 " pdb=" OG1 THR B 268 " model vdw 2.266 3.120 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 324 " model vdw 2.311 3.040 nonbonded pdb=" O ARG A 350 " pdb=" NE ARG A 350 " model vdw 2.329 3.120 ... (remaining 90906 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.055 12511 Z= 0.155 Angle : 0.745 14.221 17007 Z= 0.437 Chirality : 0.043 0.220 1862 Planarity : 0.004 0.103 2242 Dihedral : 17.059 89.870 4497 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.85 % Favored : 85.96 % Rotamer: Outliers : 3.70 % Allowed : 13.26 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % 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: -5.39 (0.16), residues: 1560 helix: -3.14 (0.22), residues: 266 sheet: -3.08 (0.25), residues: 342 loop : -4.12 (0.15), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 94 TYR 0.016 0.001 TYR A 522 PHE 0.014 0.001 PHE D 64 TRP 0.014 0.001 TRP B 93 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00280 (12509) covalent geometry : angle 0.74490 (17003) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.43668 ( 4) hydrogen bonds : bond 0.22131 ( 280) hydrogen bonds : angle 8.84036 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7724 (p0) cc_final: 0.7406 (p0) REVERT: A 581 LEU cc_start: 0.7293 (mt) cc_final: 0.7012 (mt) REVERT: B 368 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7481 (tm-30) outliers start: 48 outliers final: 29 residues processed: 268 average time/residue: 0.1008 time to fit residues: 40.5275 Evaluate side-chains 205 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 384 GLN A 561 GLN B 40 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 34 GLN E 52 GLN E 83 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110869 restraints weight = 21078.059| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.09 r_work: 0.3378 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12511 Z= 0.121 Angle : 0.664 14.422 17007 Z= 0.342 Chirality : 0.044 0.210 1862 Planarity : 0.005 0.104 2242 Dihedral : 7.170 84.444 1776 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.42 % Favored : 85.45 % Rotamer: Outliers : 4.70 % Allowed : 18.27 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % 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: -4.64 (0.18), residues: 1560 helix: -1.86 (0.27), residues: 279 sheet: -2.71 (0.25), residues: 365 loop : -3.82 (0.16), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 94 TYR 0.015 0.001 TYR A 574 PHE 0.013 0.001 PHE A 197 TRP 0.008 0.001 TRP B 93 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00272 (12509) covalent geometry : angle 0.66401 (17003) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.83524 ( 4) hydrogen bonds : bond 0.03176 ( 280) hydrogen bonds : angle 5.23158 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 0.477 Fit side-chains REVERT: A 108 ASP cc_start: 0.8239 (t0) cc_final: 0.7996 (t0) REVERT: A 230 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6101 (t80) REVERT: A 581 LEU cc_start: 0.7194 (mt) cc_final: 0.6941 (mt) REVERT: A 582 ASP cc_start: 0.7888 (t70) cc_final: 0.7540 (t70) REVERT: A 794 TYR cc_start: 0.6690 (m-80) cc_final: 0.6291 (m-80) REVERT: B 95 VAL cc_start: 0.8695 (p) cc_final: 0.8403 (m) REVERT: B 197 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: D 56 GLU cc_start: 0.8600 (pt0) cc_final: 0.8362 (pt0) REVERT: D 111 MET cc_start: 0.8611 (mmm) cc_final: 0.8394 (mmm) REVERT: D 187 GLU cc_start: 0.8998 (pt0) cc_final: 0.8769 (pt0) REVERT: E 47 ARG cc_start: 0.8423 (ptp90) cc_final: 0.7901 (mtm110) outliers start: 61 outliers final: 37 residues processed: 225 average time/residue: 0.1061 time to fit residues: 35.4362 Evaluate side-chains 206 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 83 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS E 34 GLN E 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092303 restraints weight = 21504.161| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.13 r_work: 0.3076 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12511 Z= 0.249 Angle : 0.780 14.241 17007 Z= 0.409 Chirality : 0.049 0.254 1862 Planarity : 0.005 0.100 2242 Dihedral : 7.756 85.873 1757 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.41 % Favored : 83.33 % Rotamer: Outliers : 6.78 % Allowed : 21.05 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % 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: -4.43 (0.18), residues: 1560 helix: -1.42 (0.28), residues: 297 sheet: -2.72 (0.26), residues: 355 loop : -3.74 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 767 TYR 0.028 0.002 TYR A 548 PHE 0.025 0.002 PHE A 197 TRP 0.020 0.002 TRP A 745 HIS 0.009 0.002 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00573 (12509) covalent geometry : angle 0.77945 (17003) SS BOND : bond 0.00614 ( 2) SS BOND : angle 1.11541 ( 4) hydrogen bonds : bond 0.04378 ( 280) hydrogen bonds : angle 5.18569 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 0.480 Fit side-chains REVERT: A 230 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 303 LYS cc_start: 0.8377 (tmmt) cc_final: 0.8026 (ttmt) REVERT: A 427 ASN cc_start: 0.8688 (m-40) cc_final: 0.8066 (t0) REVERT: A 471 LEU cc_start: 0.9230 (tp) cc_final: 0.8956 (tp) REVERT: A 522 TYR cc_start: 0.8128 (p90) cc_final: 0.7873 (p90) REVERT: A 550 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: A 582 ASP cc_start: 0.8252 (t70) cc_final: 0.7946 (t0) REVERT: A 780 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8217 (pp) REVERT: A 797 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: C 69 VAL cc_start: 0.6495 (OUTLIER) cc_final: 0.6172 (p) REVERT: D 56 GLU cc_start: 0.8694 (pt0) cc_final: 0.8374 (pt0) REVERT: D 102 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.6925 (t-90) REVERT: D 178 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: E 36 ASN cc_start: 0.9072 (m-40) cc_final: 0.8861 (t0) REVERT: E 72 THR cc_start: 0.8899 (m) cc_final: 0.8605 (p) REVERT: E 93 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8560 (pp) outliers start: 88 outliers final: 60 residues processed: 228 average time/residue: 0.1041 time to fit residues: 35.3891 Evaluate side-chains 224 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 0.0070 chunk 5 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095132 restraints weight = 21093.484| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.09 r_work: 0.3140 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12511 Z= 0.150 Angle : 0.699 14.203 17007 Z= 0.363 Chirality : 0.046 0.220 1862 Planarity : 0.005 0.101 2242 Dihedral : 7.208 88.251 1755 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.58 % Favored : 84.29 % Rotamer: Outliers : 6.63 % Allowed : 22.59 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % 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: -4.04 (0.19), residues: 1560 helix: -0.95 (0.29), residues: 293 sheet: -2.46 (0.27), residues: 351 loop : -3.54 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 632 TYR 0.017 0.001 TYR D 36 PHE 0.023 0.001 PHE A 197 TRP 0.011 0.001 TRP B 143 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00344 (12509) covalent geometry : angle 0.69880 (17003) SS BOND : bond 0.00175 ( 2) SS BOND : angle 1.12109 ( 4) hydrogen bonds : bond 0.03232 ( 280) hydrogen bonds : angle 4.86548 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 0.527 Fit side-chains REVERT: A 230 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 303 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8032 (ttmt) REVERT: A 427 ASN cc_start: 0.8580 (m-40) cc_final: 0.8020 (t0) REVERT: A 522 TYR cc_start: 0.7974 (p90) cc_final: 0.7620 (p90) REVERT: A 523 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8142 (m-40) REVERT: A 582 ASP cc_start: 0.8194 (t70) cc_final: 0.7909 (t0) REVERT: A 797 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: B 197 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: C 69 VAL cc_start: 0.6503 (OUTLIER) cc_final: 0.6255 (p) REVERT: D 56 GLU cc_start: 0.8637 (pt0) cc_final: 0.8298 (pt0) REVERT: D 102 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.6900 (t-90) REVERT: D 178 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7155 (mp0) outliers start: 86 outliers final: 54 residues processed: 220 average time/residue: 0.1041 time to fit residues: 34.2197 Evaluate side-chains 213 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain G residue 1281 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN E 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094921 restraints weight = 21325.025| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.14 r_work: 0.3134 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12511 Z= 0.150 Angle : 0.694 14.304 17007 Z= 0.360 Chirality : 0.047 0.375 1862 Planarity : 0.005 0.102 2242 Dihedral : 7.149 88.596 1755 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.60 % Favored : 83.27 % Rotamer: Outliers : 6.94 % Allowed : 23.36 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.19), residues: 1560 helix: -0.70 (0.30), residues: 292 sheet: -2.38 (0.27), residues: 354 loop : -3.41 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.014 0.001 TYR D 79 PHE 0.015 0.001 PHE A 197 TRP 0.010 0.001 TRP B 93 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00345 (12509) covalent geometry : angle 0.69353 (17003) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.09756 ( 4) hydrogen bonds : bond 0.03152 ( 280) hydrogen bonds : angle 4.75798 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 165 time to evaluate : 0.536 Fit side-chains REVERT: A 46 MET cc_start: 0.3786 (mmp) cc_final: 0.3362 (mmm) REVERT: A 230 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6647 (t80) REVERT: A 303 LYS cc_start: 0.8320 (tmmt) cc_final: 0.8014 (ttmt) REVERT: A 427 ASN cc_start: 0.8483 (m-40) cc_final: 0.8056 (t0) REVERT: A 522 TYR cc_start: 0.7910 (p90) cc_final: 0.7566 (p90) REVERT: A 523 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: A 560 ASP cc_start: 0.6424 (t0) cc_final: 0.6206 (t0) REVERT: A 780 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8142 (pp) REVERT: A 797 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: B 197 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: B 311 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6221 (p0) REVERT: B 343 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: C 69 VAL cc_start: 0.6545 (OUTLIER) cc_final: 0.6287 (p) REVERT: D 56 GLU cc_start: 0.8610 (pt0) cc_final: 0.8397 (pt0) REVERT: D 102 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.6942 (t-90) REVERT: E 64 MET cc_start: 0.8641 (mtm) cc_final: 0.8314 (mtp) outliers start: 90 outliers final: 62 residues processed: 233 average time/residue: 0.1029 time to fit residues: 35.8554 Evaluate side-chains 224 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain G residue 1281 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 146 optimal weight: 0.0370 chunk 116 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 540 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 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 = 0.3580 r_free = 0.3580 target = 0.118041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087454 restraints weight = 21625.350| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.11 r_work: 0.3032 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12511 Z= 0.284 Angle : 0.801 16.105 17007 Z= 0.422 Chirality : 0.051 0.309 1862 Planarity : 0.006 0.107 2242 Dihedral : 7.831 86.214 1755 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 18.01 % Favored : 81.79 % Rotamer: Outliers : 7.71 % Allowed : 24.44 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.33 % 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: -4.02 (0.19), residues: 1560 helix: -0.84 (0.29), residues: 300 sheet: -2.66 (0.26), residues: 371 loop : -3.48 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 767 TYR 0.023 0.002 TYR D 79 PHE 0.022 0.002 PHE A 675 TRP 0.017 0.002 TRP A 745 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00657 (12509) covalent geometry : angle 0.80121 (17003) SS BOND : bond 0.00232 ( 2) SS BOND : angle 1.49511 ( 4) hydrogen bonds : bond 0.04127 ( 280) hydrogen bonds : angle 5.13487 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 157 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.4038 (mmp) cc_final: 0.3627 (mmm) REVERT: A 112 GLN cc_start: 0.9027 (pt0) cc_final: 0.8817 (pm20) REVERT: A 141 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: A 230 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 370 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8388 (ptp-110) REVERT: A 427 ASN cc_start: 0.8510 (m-40) cc_final: 0.8095 (t0) REVERT: A 522 TYR cc_start: 0.8085 (p90) cc_final: 0.7716 (p90) REVERT: A 523 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8234 (m-40) REVERT: A 780 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8237 (pp) REVERT: A 797 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8252 (t0) REVERT: B 300 ASP cc_start: 0.7014 (p0) cc_final: 0.6796 (p0) REVERT: B 311 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6416 (p0) REVERT: B 343 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8585 (mt-10) REVERT: C 78 LYS cc_start: 0.9237 (mmtt) cc_final: 0.9024 (mmmm) REVERT: D 102 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: D 178 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7380 (mp0) outliers start: 100 outliers final: 66 residues processed: 235 average time/residue: 0.1085 time to fit residues: 38.0046 Evaluate side-chains 222 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 146 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain G residue 1281 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 594 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093704 restraints weight = 21232.018| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.12 r_work: 0.3100 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12511 Z= 0.139 Angle : 0.708 17.002 17007 Z= 0.367 Chirality : 0.047 0.286 1862 Planarity : 0.005 0.102 2242 Dihedral : 7.190 89.812 1753 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.54 % Favored : 83.33 % Rotamer: Outliers : 6.63 % Allowed : 25.52 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.20), residues: 1560 helix: -0.53 (0.30), residues: 298 sheet: -2.39 (0.26), residues: 368 loop : -3.36 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 632 TYR 0.016 0.001 TYR D 79 PHE 0.031 0.001 PHE A 72 TRP 0.012 0.001 TRP B 93 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00316 (12509) covalent geometry : angle 0.70743 (17003) SS BOND : bond 0.00149 ( 2) SS BOND : angle 1.24532 ( 4) hydrogen bonds : bond 0.03052 ( 280) hydrogen bonds : angle 4.75680 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 166 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: G 1285 LYS cc_start: 0.5690 (mmtt) cc_final: 0.4922 (mtmm) REVERT: A 46 MET cc_start: 0.3911 (mmp) cc_final: 0.3598 (mmm) REVERT: A 230 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 427 ASN cc_start: 0.8280 (m-40) cc_final: 0.8008 (t0) REVERT: A 523 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: A 754 TYR cc_start: 0.6961 (m-10) cc_final: 0.6726 (m-10) REVERT: A 780 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8184 (pp) REVERT: A 797 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: B 300 ASP cc_start: 0.6811 (p0) cc_final: 0.6609 (p0) REVERT: C 78 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8936 (mmmm) REVERT: D 102 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.6921 (t-90) outliers start: 86 outliers final: 63 residues processed: 232 average time/residue: 0.1014 time to fit residues: 35.2543 Evaluate side-chains 222 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 149 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092011 restraints weight = 21405.970| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.14 r_work: 0.3087 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12511 Z= 0.173 Angle : 0.756 16.797 17007 Z= 0.392 Chirality : 0.049 0.442 1862 Planarity : 0.005 0.101 2242 Dihedral : 7.126 89.446 1749 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.67 % Favored : 83.21 % Rotamer: Outliers : 6.71 % Allowed : 25.98 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.20), residues: 1560 helix: -0.43 (0.30), residues: 300 sheet: -2.31 (0.27), residues: 365 loop : -3.30 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.024 0.001 TYR D 79 PHE 0.050 0.002 PHE A 72 TRP 0.011 0.001 TRP A 576 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00395 (12509) covalent geometry : angle 0.75563 (17003) SS BOND : bond 0.00202 ( 2) SS BOND : angle 1.28642 ( 4) hydrogen bonds : bond 0.03337 ( 280) hydrogen bonds : angle 4.76759 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 158 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: G 1285 LYS cc_start: 0.5826 (mmtt) cc_final: 0.5028 (mtmm) REVERT: A 46 MET cc_start: 0.3969 (mmp) cc_final: 0.3656 (mmm) REVERT: A 123 GLU cc_start: 0.7928 (mp0) cc_final: 0.7375 (mp0) REVERT: A 230 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 427 ASN cc_start: 0.8355 (m-40) cc_final: 0.8074 (t0) REVERT: A 523 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8180 (m-40) REVERT: A 754 TYR cc_start: 0.6926 (m-10) cc_final: 0.6687 (m-10) REVERT: A 780 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 797 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.7295 (t0) REVERT: A 804 PHE cc_start: 0.7962 (p90) cc_final: 0.7592 (p90) REVERT: B 197 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 300 ASP cc_start: 0.7059 (p0) cc_final: 0.6767 (p0) REVERT: B 343 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: D 102 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: D 178 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7178 (mp0) outliers start: 87 outliers final: 70 residues processed: 224 average time/residue: 0.1000 time to fit residues: 33.8697 Evaluate side-chains 233 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 155 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092279 restraints weight = 21087.801| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.08 r_work: 0.3095 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12511 Z= 0.172 Angle : 0.753 16.217 17007 Z= 0.390 Chirality : 0.049 0.439 1862 Planarity : 0.005 0.099 2242 Dihedral : 7.128 89.855 1749 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.24 % Favored : 82.63 % Rotamer: Outliers : 6.40 % Allowed : 26.06 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.20), residues: 1560 helix: -0.39 (0.30), residues: 301 sheet: -2.33 (0.27), residues: 370 loop : -3.29 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.025 0.001 TYR D 79 PHE 0.044 0.002 PHE A 72 TRP 0.010 0.001 TRP B 93 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00393 (12509) covalent geometry : angle 0.75318 (17003) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.19233 ( 4) hydrogen bonds : bond 0.03304 ( 280) hydrogen bonds : angle 4.76476 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 155 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: G 1285 LYS cc_start: 0.6102 (mmtt) cc_final: 0.5326 (mtmm) REVERT: A 46 MET cc_start: 0.3967 (mmp) cc_final: 0.3653 (mmm) REVERT: A 123 GLU cc_start: 0.7973 (mp0) cc_final: 0.7431 (mp0) REVERT: A 230 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.6723 (t80) REVERT: A 427 ASN cc_start: 0.8352 (m-40) cc_final: 0.8127 (t0) REVERT: A 523 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: A 754 TYR cc_start: 0.7008 (m-10) cc_final: 0.6765 (m-10) REVERT: A 780 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 797 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8222 (t0) REVERT: A 804 PHE cc_start: 0.7972 (p90) cc_final: 0.7621 (p90) REVERT: B 197 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: B 300 ASP cc_start: 0.7131 (p0) cc_final: 0.6797 (p0) REVERT: B 343 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: D 102 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.6935 (t-90) REVERT: D 111 MET cc_start: 0.8358 (tpp) cc_final: 0.7858 (mpp) outliers start: 83 outliers final: 70 residues processed: 222 average time/residue: 0.1002 time to fit residues: 33.6403 Evaluate side-chains 226 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 149 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 135 optimal weight: 0.2980 chunk 68 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** B 223 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.127999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097977 restraints weight = 21179.724| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.10 r_work: 0.3182 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12511 Z= 0.122 Angle : 0.718 15.181 17007 Z= 0.367 Chirality : 0.047 0.396 1862 Planarity : 0.005 0.095 2242 Dihedral : 6.655 85.287 1748 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.45 % Favored : 84.49 % Rotamer: Outliers : 4.86 % Allowed : 27.29 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.20), residues: 1560 helix: -0.15 (0.31), residues: 295 sheet: -2.08 (0.27), residues: 371 loop : -3.15 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 632 TYR 0.015 0.001 TYR D 107 PHE 0.041 0.001 PHE A 72 TRP 0.016 0.001 TRP A 546 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00270 (12509) covalent geometry : angle 0.71813 (17003) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.11628 ( 4) hydrogen bonds : bond 0.02635 ( 280) hydrogen bonds : angle 4.56008 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.3825 (mmp) cc_final: 0.3594 (mmm) REVERT: A 230 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 274 SER cc_start: 0.8659 (t) cc_final: 0.8435 (p) REVERT: A 523 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: A 797 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.7234 (t0) REVERT: A 804 PHE cc_start: 0.7978 (p90) cc_final: 0.7613 (p90) REVERT: B 197 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: B 343 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: C 71 ASN cc_start: 0.7216 (t0) cc_final: 0.6974 (t0) REVERT: D 102 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.6955 (t-90) REVERT: D 111 MET cc_start: 0.8216 (tpp) cc_final: 0.7913 (mpp) outliers start: 63 outliers final: 53 residues processed: 219 average time/residue: 0.0989 time to fit residues: 32.3795 Evaluate side-chains 219 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 LEU Chi-restraints excluded: chain G residue 1276 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** B 223 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.121714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091184 restraints weight = 21390.188| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.12 r_work: 0.3075 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12511 Z= 0.203 Angle : 0.784 16.211 17007 Z= 0.403 Chirality : 0.050 0.424 1862 Planarity : 0.005 0.093 2242 Dihedral : 7.148 88.617 1747 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.37 % Favored : 82.50 % Rotamer: Outliers : 5.17 % Allowed : 27.68 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.20), residues: 1560 helix: -0.29 (0.30), residues: 302 sheet: -2.26 (0.27), residues: 376 loop : -3.23 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 767 TYR 0.040 0.002 TYR D 79 PHE 0.026 0.002 PHE G1278 TRP 0.014 0.001 TRP A 745 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00465 (12509) covalent geometry : angle 0.78402 (17003) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.17849 ( 4) hydrogen bonds : bond 0.03590 ( 280) hydrogen bonds : angle 4.77500 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.35 seconds wall clock time: 50 minutes 0.38 seconds (3000.38 seconds total)