Starting phenix.real_space_refine on Wed Jul 30 10:02:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_24473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_24473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_24473.map" model { file = "/net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_24473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ri4_24473/07_2025/7ri4_24473.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.077 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 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: 6.87, per 1000 atoms: 0.56 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: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.36 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: 3.88 Time building geometry restraints manager: 3.14 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: 2.220 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 28.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP B 93 HIS 0.003 0.001 HIS B 347 PHE 0.014 0.001 PHE D 64 TYR 0.016 0.001 TYR A 522 ARG 0.006 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.22131 ( 280) hydrogen bonds : angle 8.84036 ( 876) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.43668 ( 4) covalent geometry : bond 0.00280 (12509) covalent geometry : angle 0.74490 (17003) *********************** 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 : 1.281 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 273 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7238 (mtm-85) 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: 0.2114 time to fit residues: 84.1694 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 : 1.219 ------------------------------------------------------------------------------- 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 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 121 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097829 restraints weight = 21079.090| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.09 r_work: 0.3178 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12511 Z= 0.195 Angle : 0.745 14.321 17007 Z= 0.388 Chirality : 0.047 0.215 1862 Planarity : 0.005 0.104 2242 Dihedral : 7.752 76.377 1776 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.03 % Favored : 83.85 % Rotamer: Outliers : 6.17 % Allowed : 19.28 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.17), residues: 1560 helix: -1.95 (0.27), residues: 282 sheet: -2.87 (0.25), residues: 352 loop : -3.82 (0.16), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 745 HIS 0.007 0.001 HIS A 677 PHE 0.017 0.002 PHE A 565 TYR 0.019 0.002 TYR A 760 ARG 0.007 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 280) hydrogen bonds : angle 5.26123 ( 876) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.16012 ( 4) covalent geometry : bond 0.00448 (12509) covalent geometry : angle 0.74462 (17003) *********************** 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 257 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 1.459 Fit side-chains REVERT: A 108 ASP cc_start: 0.8370 (t0) cc_final: 0.8112 (t0) REVERT: A 230 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 346 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7879 (mmt180) REVERT: A 347 PHE cc_start: 0.8660 (m-10) cc_final: 0.8456 (m-80) REVERT: A 427 ASN cc_start: 0.8684 (m-40) cc_final: 0.8050 (t0) REVERT: A 522 TYR cc_start: 0.7977 (p90) cc_final: 0.7645 (p90) REVERT: A 582 ASP cc_start: 0.8096 (t70) cc_final: 0.7802 (t0) REVERT: A 794 TYR cc_start: 0.7128 (m-80) cc_final: 0.6331 (m-80) REVERT: A 797 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8186 (t0) REVERT: B 197 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 368 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: D 56 GLU cc_start: 0.8652 (pt0) cc_final: 0.8447 (pt0) REVERT: D 102 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.6951 (t-90) outliers start: 80 outliers final: 50 residues processed: 237 average time/residue: 0.2364 time to fit residues: 83.6184 Evaluate side-chains 211 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1259 LEU Chi-restraints excluded: chain G residue 1264 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 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 247 LEU Chi-restraints excluded: chain A residue 304 MET 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 444 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR 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 586 PHE Chi-restraints excluded: chain A residue 619 VAL 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 713 VAL Chi-restraints excluded: chain A residue 716 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 197 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 268 THR 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 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 180 SER 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 53 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 259 ASN ** A 561 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098603 restraints weight = 21303.214| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.12 r_work: 0.3194 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12511 Z= 0.138 Angle : 0.683 14.116 17007 Z= 0.351 Chirality : 0.045 0.205 1862 Planarity : 0.005 0.102 2242 Dihedral : 7.291 81.739 1763 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.13 % Favored : 84.74 % Rotamer: Outliers : 5.24 % Allowed : 22.36 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.18), residues: 1560 helix: -1.11 (0.30), residues: 278 sheet: -2.57 (0.26), residues: 350 loop : -3.66 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.004 0.001 HIS A 677 PHE 0.022 0.001 PHE G1278 TYR 0.014 0.001 TYR B 333 ARG 0.005 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 280) hydrogen bonds : angle 4.95213 ( 876) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.91265 ( 4) covalent geometry : bond 0.00317 (12509) covalent geometry : angle 0.68305 (17003) *********************** 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 233 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 2.177 Fit side-chains REVERT: A 230 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 303 LYS cc_start: 0.8281 (tmmt) cc_final: 0.7925 (ttmt) REVERT: A 427 ASN cc_start: 0.8603 (m-40) cc_final: 0.8063 (t0) REVERT: A 522 TYR cc_start: 0.7896 (p90) cc_final: 0.7596 (p90) REVERT: A 582 ASP cc_start: 0.8071 (t70) cc_final: 0.7794 (t0) REVERT: B 197 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: C 69 VAL cc_start: 0.6548 (OUTLIER) cc_final: 0.6247 (p) REVERT: C 78 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8945 (mmtt) REVERT: D 56 GLU cc_start: 0.8592 (pt0) cc_final: 0.8328 (pt0) REVERT: D 102 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7058 (t-90) outliers start: 68 outliers final: 51 residues processed: 218 average time/residue: 0.2928 time to fit residues: 96.6837 Evaluate side-chains 208 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 369 MET 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 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 549 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 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 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 540 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089697 restraints weight = 21373.743| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.09 r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12511 Z= 0.247 Angle : 0.781 14.724 17007 Z= 0.409 Chirality : 0.049 0.275 1862 Planarity : 0.005 0.100 2242 Dihedral : 8.041 82.821 1763 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.50 % Favored : 82.31 % Rotamer: Outliers : 7.48 % Allowed : 22.82 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 4.69 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.19), residues: 1560 helix: -1.16 (0.28), residues: 300 sheet: -2.81 (0.24), residues: 392 loop : -3.61 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 745 HIS 0.007 0.001 HIS A 280 PHE 0.021 0.002 PHE A 675 TYR 0.020 0.002 TYR A 548 ARG 0.005 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 280) hydrogen bonds : angle 5.16327 ( 876) SS BOND : bond 0.00237 ( 2) SS BOND : angle 1.33596 ( 4) covalent geometry : bond 0.00568 (12509) covalent geometry : angle 0.78083 (17003) *********************** 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 260 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 163 time to evaluate : 1.394 Fit side-chains REVERT: G 1285 LYS cc_start: 0.5989 (mmtt) cc_final: 0.5212 (mtmm) REVERT: A 141 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: A 230 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 370 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8362 (ptp-110) REVERT: A 427 ASN cc_start: 0.8511 (m-40) cc_final: 0.8037 (t0) REVERT: A 522 TYR cc_start: 0.8099 (p90) cc_final: 0.7787 (p90) REVERT: A 523 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: A 560 ASP cc_start: 0.6667 (t0) cc_final: 0.6349 (t0) REVERT: A 797 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.7342 (t0) REVERT: A 804 PHE cc_start: 0.7969 (p90) cc_final: 0.7520 (p90) REVERT: B 111 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 300 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6610 (p0) REVERT: C 78 LYS cc_start: 0.9337 (mmtt) cc_final: 0.9106 (mmtt) REVERT: D 102 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: D 183 GLU cc_start: 0.8683 (tt0) cc_final: 0.8467 (tt0) REVERT: E 72 THR cc_start: 0.8763 (m) cc_final: 0.8513 (p) outliers start: 97 outliers final: 63 residues processed: 234 average time/residue: 0.2567 time to fit residues: 89.5932 Evaluate side-chains 223 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 247 LEU 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 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 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 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 111 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 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 249 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 ASP 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 69 GLN Chi-restraints excluded: chain D residue 102 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094921 restraints weight = 21091.551| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.11 r_work: 0.3133 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12511 Z= 0.132 Angle : 0.692 14.185 17007 Z= 0.358 Chirality : 0.046 0.270 1862 Planarity : 0.005 0.101 2242 Dihedral : 7.369 89.835 1759 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.96 % Favored : 83.91 % Rotamer: Outliers : 6.78 % Allowed : 24.67 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.19), residues: 1560 helix: -0.74 (0.30), residues: 295 sheet: -2.44 (0.26), residues: 354 loop : -3.45 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS A 280 PHE 0.022 0.001 PHE A 197 TYR 0.018 0.001 TYR D 36 ARG 0.007 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 280) hydrogen bonds : angle 4.78086 ( 876) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.14580 ( 4) covalent geometry : bond 0.00303 (12509) covalent geometry : angle 0.69164 (17003) *********************** 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 250 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 162 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: G 1285 LYS cc_start: 0.5995 (mmtt) cc_final: 0.5258 (mtmm) REVERT: A 230 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 427 ASN cc_start: 0.8391 (m-40) cc_final: 0.8073 (t0) REVERT: A 754 TYR cc_start: 0.6910 (m-10) cc_final: 0.6630 (m-10) REVERT: A 797 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 804 PHE cc_start: 0.8028 (p90) cc_final: 0.7543 (p90) REVERT: B 197 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 300 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6320 (p0) REVERT: D 102 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: D 111 MET cc_start: 0.8434 (tpp) cc_final: 0.7605 (mpp) REVERT: D 227 MET cc_start: 0.8675 (mtt) cc_final: 0.8360 (mtt) outliers start: 88 outliers final: 59 residues processed: 229 average time/residue: 0.2705 time to fit residues: 92.6883 Evaluate side-chains 212 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 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 247 LEU 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 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 483 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU 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 715 SER 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 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 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 ASP 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 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 52 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.0030 chunk 153 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 54 optimal weight: 0.0060 overall best weight: 0.7608 ------------------------------------------------------------------------------- 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 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096346 restraints weight = 21595.448| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.13 r_work: 0.3158 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12511 Z= 0.124 Angle : 0.681 14.608 17007 Z= 0.350 Chirality : 0.045 0.244 1862 Planarity : 0.005 0.105 2242 Dihedral : 7.149 88.751 1759 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.15 % Favored : 83.72 % Rotamer: Outliers : 6.40 % Allowed : 25.60 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.20), residues: 1560 helix: -0.40 (0.31), residues: 288 sheet: -2.33 (0.26), residues: 372 loop : -3.28 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.002 0.001 HIS A 280 PHE 0.014 0.001 PHE A 197 TYR 0.017 0.001 TYR D 36 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 280) hydrogen bonds : angle 4.64682 ( 876) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.06265 ( 4) covalent geometry : bond 0.00283 (12509) covalent geometry : angle 0.68112 (17003) *********************** 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 246 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 4.663 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.3831 (mmp) cc_final: 0.3441 (mmm) REVERT: A 230 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6451 (t80) REVERT: A 427 ASN cc_start: 0.8360 (m-40) cc_final: 0.8079 (t0) REVERT: A 523 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: A 797 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.7082 (t0) REVERT: A 804 PHE cc_start: 0.7999 (p90) cc_final: 0.7508 (p90) REVERT: B 197 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 300 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6440 (p0) REVERT: B 343 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: C 78 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8860 (mmmm) REVERT: D 102 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7099 (t-90) outliers start: 83 outliers final: 61 residues processed: 227 average time/residue: 0.2917 time to fit residues: 100.2403 Evaluate side-chains 220 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 110 LEU 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 247 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 VAL 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 480 VAL Chi-restraints excluded: chain A residue 483 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 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 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 152 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 268 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ASP 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 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 30 ASN Chi-restraints excluded: chain D residue 52 ILE 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 D residue 186 THR 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 Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 87 optimal weight: 0.0030 overall best weight: 1.5692 ------------------------------------------------------------------------------- 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093317 restraints weight = 21306.107| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.12 r_work: 0.3108 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12511 Z= 0.170 Angle : 0.722 13.870 17007 Z= 0.374 Chirality : 0.046 0.218 1862 Planarity : 0.005 0.102 2242 Dihedral : 7.344 89.314 1758 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.73 % Favored : 83.14 % Rotamer: Outliers : 6.63 % Allowed : 25.44 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.20), residues: 1560 helix: -0.49 (0.30), residues: 300 sheet: -2.33 (0.26), residues: 375 loop : -3.31 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 745 HIS 0.003 0.001 HIS A 280 PHE 0.020 0.001 PHE D 64 TYR 0.016 0.001 TYR A 522 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 280) hydrogen bonds : angle 4.75053 ( 876) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.11151 ( 4) covalent geometry : bond 0.00391 (12509) covalent geometry : angle 0.72222 (17003) *********************** 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 241 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 155 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.3888 (mmp) cc_final: 0.3525 (mmm) REVERT: A 230 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6543 (t80) REVERT: A 427 ASN cc_start: 0.8387 (m-40) cc_final: 0.8077 (t0) REVERT: A 523 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (m-40) REVERT: A 754 TYR cc_start: 0.6949 (m-10) cc_final: 0.6667 (m-10) REVERT: A 797 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.7084 (t0) REVERT: A 804 PHE cc_start: 0.8043 (p90) cc_final: 0.7559 (p90) REVERT: B 197 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: B 300 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6431 (p0) REVERT: C 78 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8962 (mmmm) REVERT: D 102 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7055 (t-90) REVERT: E 92 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8852 (t) outliers start: 86 outliers final: 67 residues processed: 220 average time/residue: 0.2129 time to fit residues: 70.5013 Evaluate side-chains 223 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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 247 LEU 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 370 ARG 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 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 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 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 268 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ASP 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 27 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 69 GLN 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 D residue 186 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 Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3655 r_free = 0.3655 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093614 restraints weight = 21375.599| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.13 r_work: 0.3111 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12511 Z= 0.157 Angle : 0.712 13.772 17007 Z= 0.368 Chirality : 0.046 0.208 1862 Planarity : 0.005 0.099 2242 Dihedral : 7.298 88.636 1758 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.47 % Favored : 83.40 % Rotamer: Outliers : 7.09 % Allowed : 25.52 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1560 helix: -0.40 (0.31), residues: 301 sheet: -2.21 (0.27), residues: 371 loop : -3.27 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 93 HIS 0.004 0.001 HIS A 280 PHE 0.018 0.001 PHE D 64 TYR 0.017 0.001 TYR D 36 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 280) hydrogen bonds : angle 4.69641 ( 876) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.09883 ( 4) covalent geometry : bond 0.00360 (12509) covalent geometry : angle 0.71145 (17003) *********************** 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 247 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 155 time to evaluate : 1.269 Fit side-chains REVERT: A 46 MET cc_start: 0.3910 (mmp) cc_final: 0.3565 (mmm) REVERT: A 230 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.6610 (t80) REVERT: A 427 ASN cc_start: 0.8372 (m-40) cc_final: 0.8106 (t0) REVERT: A 523 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: A 754 TYR cc_start: 0.7060 (m-10) cc_final: 0.6787 (m-10) REVERT: A 797 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.7293 (t0) REVERT: A 804 PHE cc_start: 0.8059 (p90) cc_final: 0.7592 (p90) REVERT: B 197 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 300 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6503 (p0) REVERT: B 343 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: C 65 TYR cc_start: 0.7901 (t80) cc_final: 0.7688 (t80) REVERT: C 78 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8973 (mmmm) REVERT: D 102 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7079 (t-90) REVERT: E 92 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8877 (t) REVERT: E 101 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7494 (tt) outliers start: 92 outliers final: 73 residues processed: 227 average time/residue: 0.2381 time to fit residues: 82.1638 Evaluate side-chains 231 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 149 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 88 VAL 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 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 247 LEU 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 704 ASP 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 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 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 268 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ASP 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 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 52 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 108 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR 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 Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095897 restraints weight = 21176.323| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.11 r_work: 0.3147 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3809 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= 0.129 Angle : 0.698 13.969 17007 Z= 0.358 Chirality : 0.045 0.208 1862 Planarity : 0.005 0.096 2242 Dihedral : 7.089 86.684 1757 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.22 % Favored : 83.72 % Rotamer: Outliers : 6.40 % Allowed : 26.14 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.20), residues: 1560 helix: -0.27 (0.31), residues: 295 sheet: -2.05 (0.28), residues: 369 loop : -3.16 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 93 HIS 0.002 0.001 HIS A 280 PHE 0.015 0.001 PHE D 64 TYR 0.020 0.001 TYR D 107 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 280) hydrogen bonds : angle 4.59369 ( 876) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.02761 ( 4) covalent geometry : bond 0.00293 (12509) covalent geometry : angle 0.69762 (17003) *********************** 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 242 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 159 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.3823 (mmp) cc_final: 0.3534 (mmm) REVERT: A 230 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 427 ASN cc_start: 0.8363 (m-40) cc_final: 0.8157 (t0) REVERT: A 523 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7929 (m-40) REVERT: A 632 ARG cc_start: 0.8049 (ptt90) cc_final: 0.7769 (ptt90) REVERT: A 754 TYR cc_start: 0.6984 (m-10) cc_final: 0.6742 (m-10) REVERT: A 797 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.7220 (t0) REVERT: A 804 PHE cc_start: 0.8057 (p90) cc_final: 0.7596 (p90) REVERT: B 197 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 300 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6424 (p0) REVERT: B 343 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: C 71 ASN cc_start: 0.7276 (t0) cc_final: 0.7032 (t0) REVERT: D 102 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7093 (t-90) REVERT: D 227 MET cc_start: 0.9122 (mtm) cc_final: 0.8643 (mtm) REVERT: E 92 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (t) REVERT: E 101 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7475 (tt) outliers start: 83 outliers final: 67 residues processed: 222 average time/residue: 0.2395 time to fit residues: 78.9137 Evaluate side-chains 226 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 88 VAL 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 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 247 LEU 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 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 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 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 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 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ASP 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 379 LEU 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 52 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 108 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 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 Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096034 restraints weight = 21113.488| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.12 r_work: 0.3150 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3842 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= 0.131 Angle : 0.704 14.141 17007 Z= 0.362 Chirality : 0.046 0.206 1862 Planarity : 0.005 0.093 2242 Dihedral : 7.053 85.544 1757 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.28 % Favored : 83.65 % Rotamer: Outliers : 6.01 % Allowed : 26.75 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.20), residues: 1560 helix: -0.15 (0.32), residues: 291 sheet: -2.10 (0.27), residues: 376 loop : -3.15 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 93 HIS 0.002 0.001 HIS A 280 PHE 0.014 0.001 PHE D 64 TYR 0.033 0.001 TYR D 107 ARG 0.007 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 280) hydrogen bonds : angle 4.56410 ( 876) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.97149 ( 4) covalent geometry : bond 0.00297 (12509) covalent geometry : angle 0.70384 (17003) ********************** 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 239 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 161 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: G 1267 GLU cc_start: 0.8042 (pp20) cc_final: 0.7505 (pp20) REVERT: G 1297 ARG cc_start: 0.8936 (tpt90) cc_final: 0.8659 (tpt90) REVERT: A 46 MET cc_start: 0.3664 (mmp) cc_final: 0.3390 (mmm) REVERT: A 230 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 427 ASN cc_start: 0.8384 (m-40) cc_final: 0.8150 (t0) REVERT: A 523 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7936 (m-40) REVERT: A 702 SER cc_start: 0.8118 (t) cc_final: 0.7898 (t) REVERT: A 754 TYR cc_start: 0.6957 (m-10) cc_final: 0.6715 (m-10) REVERT: A 797 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.7191 (t0) REVERT: A 804 PHE cc_start: 0.8059 (p90) cc_final: 0.7591 (p90) REVERT: B 197 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 300 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6466 (p0) REVERT: B 343 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8628 (mm-30) REVERT: C 71 ASN cc_start: 0.7260 (t0) cc_final: 0.7047 (t0) REVERT: D 102 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7105 (t-90) REVERT: D 111 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7615 (mtp) REVERT: D 219 GLU cc_start: 0.8104 (tt0) cc_final: 0.7825 (tt0) REVERT: D 227 MET cc_start: 0.9128 (mtm) cc_final: 0.8636 (mtm) REVERT: E 101 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7408 (tt) outliers start: 78 outliers final: 66 residues processed: 222 average time/residue: 0.2514 time to fit residues: 83.4184 Evaluate side-chains 227 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 88 VAL 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 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 247 LEU 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 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 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 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 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 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ASP 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 379 LEU 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 52 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 108 VAL Chi-restraints excluded: chain D residue 111 MET 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 Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 0.0170 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 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 = 0.3717 r_free = 0.3717 target = 0.128831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098905 restraints weight = 21199.067| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.09 r_work: 0.3195 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3726 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= 0.117 Angle : 0.696 14.498 17007 Z= 0.355 Chirality : 0.045 0.206 1862 Planarity : 0.005 0.088 2242 Dihedral : 6.829 82.620 1757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.03 % Favored : 83.91 % Rotamer: Outliers : 5.78 % Allowed : 26.68 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.21), residues: 1560 helix: -0.06 (0.32), residues: 292 sheet: -2.00 (0.27), residues: 377 loop : -3.08 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.003 0.001 HIS C 51 PHE 0.013 0.001 PHE D 64 TYR 0.036 0.001 TYR D 107 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 280) hydrogen bonds : angle 4.43906 ( 876) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.90662 ( 4) covalent geometry : bond 0.00264 (12509) covalent geometry : angle 0.69580 (17003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6924.07 seconds wall clock time: 125 minutes 29.76 seconds (7529.76 seconds total)