Starting phenix.real_space_refine on Sat Sep 12 23:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2026/5gam_8011.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 169 5.49 5 S 56 5.16 5 C 11662 2.51 5 N 3310 2.21 5 O 3926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19123 Number of models: 1 Model: "" Number of chains: 13 Chain: "U" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNAv2': 141} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 64, 'rna3p_pyr': 58} Link IDs: {'rna2p': 18, 'rna3p': 122} Chain breaks: 2 Chain: "A" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4702 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 39, 'TRANS': 550} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 8, 'GLU:plan': 19, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 6450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6450 Classifications: {'peptide': 855} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'CIS': 8, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 800} Chain breaks: 3 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 34, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 15, 'PHE:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'TRP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 265 Chain: "W" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 532 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain breaks: 1 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "x" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.20 Number of scatterers: 19123 At special positions: 0 Unit cell: (138.71, 143, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 169 15.00 O 3926 8.00 N 3310 7.00 C 11662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.23 Conformation dependent library (CDL) restraints added in 652.3 milliseconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3842 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 39.5% alpha, 0.0% beta 54 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 110 through 124 removed outlier: 4.522A pdb=" N ARG A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 3.789A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 4.046A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 209 through 231 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.726A pdb=" N MET A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.767A pdb=" N LYS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 4.193A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.519A pdb=" N ASN A 487 " --> pdb=" O PRO A 483 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 515 through 535 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 616 through 641 Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.696A pdb=" N LEU A 663 " --> pdb=" O HIS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 692 removed outlier: 3.976A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 731 Proline residue: A 720 - end of helix Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.622A pdb=" N MET C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.523A pdb=" N THR C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.748A pdb=" N LEU C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.935A pdb=" N TRP C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.893A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.195A pdb=" N VAL C 436 " --> pdb=" O GLN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 458 removed outlier: 4.210A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 518 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 614 through 629 Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 745 through 757 Processing helix chain 'C' and resid 759 through 766 Processing helix chain 'C' and resid 791 through 805 removed outlier: 3.828A pdb=" N ILE C 795 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 799 " --> pdb=" O ILE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 853 Proline residue: C 840 - end of helix removed outlier: 4.115A pdb=" N LYS C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 883 removed outlier: 3.778A pdb=" N ARG C 883 " --> pdb=" O LEU C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 912 removed outlier: 4.043A pdb=" N ALA C 912 " --> pdb=" O VAL C 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 908 through 912' Processing helix chain 'C' and resid 913 through 922 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.927A pdb=" N ARG C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 998 Processing helix chain 'b' and resid 12 through 16 Processing helix chain 'e' and resid 12 through 24 Processing helix chain 'e' and resid 84 through 87 Processing helix chain 'f' and resid 14 through 22 removed outlier: 3.660A pdb=" N PHE f 18 " --> pdb=" O ASN f 14 " (cutoff:3.500A) Processing helix chain 'x' and resid 202 through 218 Processing helix chain 'd' and resid 5 through 15 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 75 through 80 Processing helix chain 'h' and resid 2 through 10 removed outlier: 3.887A pdb=" N PHE h 6 " --> pdb=" O LYS h 2 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 107 Processing helix chain 'j' and resid 16 through 29 Processing helix chain 'j' and resid 31 through 41 removed outlier: 3.775A pdb=" N ASN j 35 " --> pdb=" O MET j 31 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2709 1.32 - 1.44: 6064 1.44 - 1.57: 10660 1.57 - 1.69: 341 1.69 - 1.82: 96 Bond restraints: 19870 Sorted by residual: bond pdb=" CA TYR A 403 " pdb=" C TYR A 403 " ideal model delta sigma weight residual 1.524 1.585 -0.060 8.80e-03 1.29e+04 4.70e+01 bond pdb=" CA ILE A 719 " pdb=" CB ILE A 719 " ideal model delta sigma weight residual 1.537 1.560 -0.023 5.00e-03 4.00e+04 2.10e+01 bond pdb=" N ASN A 404 " pdb=" CA ASN A 404 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.29e-02 6.01e+03 1.87e+01 bond pdb=" C LEU A 631 " pdb=" O LEU A 631 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C5 GTP C1101 " pdb=" C6 GTP C1101 " ideal model delta sigma weight residual 1.390 1.468 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 19865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 24173 2.30 - 4.60: 3170 4.60 - 6.90: 360 6.90 - 9.21: 65 9.21 - 11.51: 20 Bond angle restraints: 27788 Sorted by residual: angle pdb=" N ASN C 259 " pdb=" CA ASN C 259 " pdb=" C ASN C 259 " ideal model delta sigma weight residual 111.14 121.27 -10.13 1.08e+00 8.57e-01 8.79e+01 angle pdb=" C GLU C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.89 129.10 -9.21 1.02e+00 9.61e-01 8.16e+01 angle pdb=" O ILE A 719 " pdb=" C ILE A 719 " pdb=" N PRO A 720 " ideal model delta sigma weight residual 120.42 126.03 -5.61 6.40e-01 2.44e+00 7.68e+01 angle pdb=" N ILE A 719 " pdb=" CA ILE A 719 " pdb=" CB ILE A 719 " ideal model delta sigma weight residual 110.52 115.93 -5.41 6.70e-01 2.23e+00 6.52e+01 angle pdb=" N ILE C 379 " pdb=" CA ILE C 379 " pdb=" CB ILE C 379 " ideal model delta sigma weight residual 110.50 115.08 -4.58 6.30e-01 2.52e+00 5.29e+01 ... (remaining 27783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 10859 35.27 - 70.55: 679 70.55 - 105.82: 28 105.82 - 141.10: 7 141.10 - 176.37: 11 Dihedral angle restraints: 11584 sinusoidal: 5664 harmonic: 5920 Sorted by residual: dihedral pdb=" C4' G U 27 " pdb=" C3' G U 27 " pdb=" C2' G U 27 " pdb=" C1' G U 27 " ideal model delta sinusoidal sigma weight residual 36.34 -40.31 76.65 1 3.10e+00 1.04e-01 7.68e+02 dihedral pdb=" C4' U U 96 " pdb=" C3' U U 96 " pdb=" C2' U U 96 " pdb=" C1' U U 96 " ideal model delta sinusoidal sigma weight residual 36.34 -39.15 75.50 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' G U 32 " pdb=" C3' G U 32 " pdb=" C2' G U 32 " pdb=" C1' G U 32 " ideal model delta sinusoidal sigma weight residual 36.35 -37.92 74.26 1 3.10e+00 1.04e-01 7.28e+02 ... (remaining 11581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2348 0.098 - 0.195: 622 0.195 - 0.293: 356 0.293 - 0.391: 35 0.391 - 0.489: 14 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C3' G U 114 " pdb=" C4' G U 114 " pdb=" O3' G U 114 " pdb=" C2' G U 114 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" C3' G U 62 " pdb=" C4' G U 62 " pdb=" O3' G U 62 " pdb=" C2' G U 62 " both_signs ideal model delta sigma weight residual False -2.50 -2.02 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA PHE A 506 " pdb=" N PHE A 506 " pdb=" C PHE A 506 " pdb=" CB PHE A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3372 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 839 " -0.095 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO C 840 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO C 840 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 840 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C U 108 " 0.006 2.00e-02 2.50e+03 2.93e-02 1.93e+01 pdb=" N1 C U 108 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C U 108 " 0.009 2.00e-02 2.50e+03 pdb=" O2 C U 108 " 0.029 2.00e-02 2.50e+03 pdb=" N3 C U 108 " -0.074 2.00e-02 2.50e+03 pdb=" C4 C U 108 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C U 108 " 0.033 2.00e-02 2.50e+03 pdb=" C5 C U 108 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C U 108 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 87 " -0.005 2.00e-02 2.50e+03 2.30e-02 1.59e+01 pdb=" N9 G U 87 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G U 87 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G U 87 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G U 87 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G U 87 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G U 87 " -0.046 2.00e-02 2.50e+03 pdb=" N1 G U 87 " 0.058 2.00e-02 2.50e+03 pdb=" C2 G U 87 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U 87 " -0.025 2.00e-02 2.50e+03 pdb=" N3 G U 87 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G U 87 " -0.003 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 94 2.56 - 3.15: 15104 3.15 - 3.73: 32949 3.73 - 4.32: 42868 4.32 - 4.90: 68323 Nonbonded interactions: 159338 Sorted by model distance: nonbonded pdb=" O2' U U 74 " pdb=" OP2 U U 76 " model vdw 1.976 3.040 nonbonded pdb=" CD1 LEU A 139 " pdb=" CD2 TYR A 193 " model vdw 2.154 3.760 nonbonded pdb=" N GLU A 467 " pdb=" OE1 GLU A 467 " model vdw 2.215 3.120 nonbonded pdb=" O2' C U 12 " pdb=" O4' A U 13 " model vdw 2.229 3.040 nonbonded pdb=" OP2 U U 33 " pdb=" OG1 THR A 296 " model vdw 2.264 3.040 ... (remaining 159333 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.220 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 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 : 0.008 0.078 19870 Z= 0.542 Angle : 1.531 11.508 27788 Z= 0.977 Chirality : 0.114 0.489 3375 Planarity : 0.008 0.143 2884 Dihedral : 20.632 176.373 7742 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 1.83 % Allowed : 9.97 % Favored : 88.20 % Rotamer: Outliers : 6.60 % Allowed : 11.19 % Favored : 82.21 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.94 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.16), residues: 1966 helix: 0.44 (0.16), residues: 707 sheet: -3.28 (0.23), residues: 291 loop : -3.44 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 883 TYR 0.029 0.003 TYR C 354 PHE 0.032 0.003 PHE A 201 TRP 0.036 0.004 TRP C 933 HIS 0.011 0.002 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.54 (19870) covalent geometry : angle 1.53062 / 0.98 (27788) hydrogen bonds : bond 0.13956 / 7.00 ( 616) hydrogen bonds : angle 6.25736 / 2.46 ( 1661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 548 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6731 (mmm) cc_final: 0.6440 (mpp) REVERT: A 168 LEU cc_start: 0.8297 (tp) cc_final: 0.7783 (tp) REVERT: A 172 ILE cc_start: 0.8771 (mt) cc_final: 0.8470 (mt) REVERT: A 199 ILE cc_start: 0.7803 (tp) cc_final: 0.7556 (mp) REVERT: A 278 ASP cc_start: 0.9658 (m-30) cc_final: 0.9231 (t0) REVERT: A 283 SER cc_start: 0.8188 (p) cc_final: 0.7987 (t) REVERT: A 284 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5840 (tpp80) REVERT: A 364 TYR cc_start: 0.2028 (OUTLIER) cc_final: 0.1804 (m-80) REVERT: A 374 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 375 PHE cc_start: 0.8330 (m-80) cc_final: 0.8084 (m-80) REVERT: A 417 TYR cc_start: 0.1475 (t80) cc_final: 0.0512 (t80) REVERT: A 533 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 572 CYS cc_start: 0.8369 (m) cc_final: 0.7709 (m) REVERT: A 635 THR cc_start: 0.8901 (p) cc_final: 0.8657 (m) REVERT: A 643 ASN cc_start: 0.9203 (m-40) cc_final: 0.8725 (p0) REVERT: A 689 TYR cc_start: 0.7975 (t80) cc_final: 0.7738 (t80) REVERT: C 113 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7981 (mt) REVERT: C 176 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6377 (ptp90) REVERT: C 193 LEU cc_start: 0.8373 (tp) cc_final: 0.8129 (tp) REVERT: C 194 ASN cc_start: 0.7076 (m-40) cc_final: 0.6770 (m110) REVERT: C 196 SER cc_start: 0.7722 (p) cc_final: 0.7390 (p) REVERT: C 264 CYS cc_start: 0.7247 (m) cc_final: 0.6394 (m) REVERT: C 387 TYR cc_start: 0.8444 (m-80) cc_final: 0.7808 (m-80) REVERT: C 431 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: C 442 CYS cc_start: 0.6445 (t) cc_final: 0.6231 (m) REVERT: C 538 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8530 (tp30) REVERT: C 596 ASP cc_start: 0.7955 (m-30) cc_final: 0.7724 (t0) REVERT: C 675 THR cc_start: 0.7996 (p) cc_final: 0.7796 (t) REVERT: C 834 MET cc_start: 0.8752 (mmm) cc_final: 0.8532 (ptt) REVERT: C 842 MET cc_start: 0.9158 (mmm) cc_final: 0.8771 (tpp) REVERT: C 889 TYR cc_start: 0.8078 (m-80) cc_final: 0.7869 (m-10) REVERT: C 908 VAL cc_start: 0.7457 (t) cc_final: 0.7219 (t) REVERT: b 78 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7981 (tm-30) REVERT: b 100 LYS cc_start: 0.8756 (pttt) cc_final: 0.8511 (mmtt) REVERT: e 47 ASP cc_start: 0.8299 (t70) cc_final: 0.8064 (t70) REVERT: e 77 LEU cc_start: 0.6906 (tt) cc_final: 0.6503 (tp) REVERT: f 18 PHE cc_start: 0.8885 (t80) cc_final: 0.8684 (t80) REVERT: f 49 PHE cc_start: 0.9288 (m-80) cc_final: 0.8847 (m-80) REVERT: f 75 CYS cc_start: 0.8537 (p) cc_final: 0.8293 (p) REVERT: f 77 ASN cc_start: 0.7661 (m-40) cc_final: 0.7148 (m-40) REVERT: g 4 THR cc_start: 0.8200 (p) cc_final: 0.7975 (t) REVERT: g 25 VAL cc_start: 0.5439 (t) cc_final: 0.4689 (t) REVERT: g 30 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7652 (tpt90) REVERT: g 33 ASP cc_start: 0.7013 (p0) cc_final: 0.6734 (p0) REVERT: g 36 LEU cc_start: 0.9148 (tp) cc_final: 0.8825 (tt) REVERT: g 45 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6623 (mp0) REVERT: g 66 ASN cc_start: 0.8661 (t0) cc_final: 0.8219 (m-40) REVERT: g 67 SER cc_start: 0.8758 (p) cc_final: 0.8481 (p) REVERT: d 23 LEU cc_start: 0.8587 (mt) cc_final: 0.8387 (mp) REVERT: d 34 VAL cc_start: 0.7720 (t) cc_final: 0.7435 (t) REVERT: d 41 ASN cc_start: 0.6866 (m110) cc_final: 0.6227 (m-40) REVERT: d 60 ASP cc_start: 0.8931 (m-30) cc_final: 0.8683 (p0) REVERT: d 62 ILE cc_start: 0.6793 (tt) cc_final: 0.6562 (tp) REVERT: d 63 PHE cc_start: 0.7322 (t80) cc_final: 0.7060 (t80) REVERT: d 70 LYS cc_start: 0.8914 (tttm) cc_final: 0.8455 (ttmm) REVERT: h 18 GLU cc_start: 0.9005 (tt0) cc_final: 0.8719 (tm-30) REVERT: h 20 LYS cc_start: 0.2823 (OUTLIER) cc_final: 0.2478 (tptt) REVERT: h 39 ILE cc_start: 0.9255 (mt) cc_final: 0.8801 (tt) REVERT: h 90 ASN cc_start: 0.8001 (p0) cc_final: 0.7545 (p0) REVERT: h 94 GLN cc_start: 0.9096 (mt0) cc_final: 0.8875 (mt0) REVERT: j 35 ASN cc_start: 0.9431 (t0) cc_final: 0.8977 (m110) REVERT: j 62 ASP cc_start: 0.8001 (p0) cc_final: 0.7432 (p0) REVERT: j 90 PHE cc_start: 0.9339 (m-80) cc_final: 0.9106 (t80) REVERT: j 92 SER cc_start: 0.9159 (m) cc_final: 0.8749 (p) REVERT: j 93 LYS cc_start: 0.7713 (mttp) cc_final: 0.7419 (mtmt) REVERT: j 101 VAL cc_start: 0.8295 (t) cc_final: 0.7882 (p) REVERT: j 106 LYS cc_start: 0.9212 (tttt) cc_final: 0.8983 (tptt) outliers start: 108 outliers final: 34 residues processed: 626 average time/residue: 0.1387 time to fit residues: 131.6381 Evaluate side-chains 416 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 770 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain h residue 20 LYS Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain j residue 24 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 HIS A 216 GLN A 310 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 344 ASN A 392 ASN A 412 GLN A 559 GLN A 576 HIS A 617 ASN A 654 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN C 260 ASN C 289 ASN C 355 HIS C 418 GLN C 423 HIS C 431 GLN C 554 HIS ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN b 14 ASN f 54 ASN f 77 ASN d 41 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 94 GLN j 28 HIS j 52 HIS ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.087050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.063633 restraints weight = 71415.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065455 restraints weight = 36575.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066633 restraints weight = 24083.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067380 restraints weight = 18639.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067738 restraints weight = 15952.613| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19870 Z= 0.257 Angle : 1.215 15.918 27788 Z= 0.533 Chirality : 0.098 1.613 3375 Planarity : 0.007 0.093 2884 Dihedral : 19.555 174.336 4239 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.92 % Favored : 92.83 % Rotamer: Outliers : 5.75 % Allowed : 19.13 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.19), residues: 1966 helix: 1.95 (0.20), residues: 705 sheet: -2.64 (0.24), residues: 321 loop : -2.86 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 64 TYR 0.036 0.002 TYR C 791 PHE 0.026 0.002 PHE C 212 TRP 0.044 0.002 TRP C 933 HIS 0.008 0.001 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 (19870) covalent geometry : angle 1.21452 / 0.53 (27788) hydrogen bonds : bond 0.07653 / 3.86 ( 616) hydrogen bonds : angle 4.41079 / 1.74 ( 1661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 403 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.9170 (tp) cc_final: 0.8746 (tp) REVERT: A 278 ASP cc_start: 0.7980 (m-30) cc_final: 0.7565 (t0) REVERT: A 283 SER cc_start: 0.8671 (p) cc_final: 0.8310 (t) REVERT: A 284 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7193 (tpp80) REVERT: A 417 TYR cc_start: 0.5816 (t80) cc_final: 0.5527 (t80) REVERT: A 484 PHE cc_start: 0.7843 (t80) cc_final: 0.7563 (t80) REVERT: A 493 MET cc_start: 0.8167 (mtt) cc_final: 0.7756 (mtt) REVERT: A 630 LYS cc_start: 0.8916 (tptm) cc_final: 0.8110 (tptp) REVERT: A 631 LEU cc_start: 0.9351 (mt) cc_final: 0.9112 (mt) REVERT: A 634 ASP cc_start: 0.8181 (m-30) cc_final: 0.7257 (m-30) REVERT: C 113 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8670 (mt) REVERT: C 139 ILE cc_start: 0.9419 (mt) cc_final: 0.9196 (pt) REVERT: C 264 CYS cc_start: 0.8699 (OUTLIER) cc_final: 0.6529 (m) REVERT: C 331 TYR cc_start: 0.8634 (m-80) cc_final: 0.7667 (m-10) REVERT: C 387 TYR cc_start: 0.8172 (m-80) cc_final: 0.7362 (m-80) REVERT: C 439 ILE cc_start: 0.9141 (mt) cc_final: 0.8885 (mt) REVERT: C 502 LEU cc_start: 0.9040 (mt) cc_final: 0.8665 (mt) REVERT: C 653 ASP cc_start: 0.7991 (t0) cc_final: 0.7761 (t0) REVERT: C 658 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8077 (t0) REVERT: C 674 LEU cc_start: 0.8672 (mp) cc_final: 0.8459 (mp) REVERT: C 842 MET cc_start: 0.8299 (mmm) cc_final: 0.8009 (tpp) REVERT: C 962 LEU cc_start: 0.8664 (tp) cc_final: 0.8400 (tp) REVERT: C 968 MET cc_start: 0.8467 (mmm) cc_final: 0.8239 (mmm) REVERT: b 18 TYR cc_start: 0.7566 (m-80) cc_final: 0.6974 (m-80) REVERT: b 33 GLN cc_start: 0.8077 (mp10) cc_final: 0.7574 (mm-40) REVERT: b 90 GLU cc_start: 0.8229 (tp30) cc_final: 0.7938 (tp30) REVERT: b 94 SER cc_start: 0.8996 (p) cc_final: 0.8409 (m) REVERT: e 23 GLN cc_start: 0.8602 (mt0) cc_final: 0.8214 (pt0) REVERT: g 11 MET cc_start: 0.7584 (mmm) cc_final: 0.7242 (tpt) REVERT: g 61 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (p) REVERT: g 66 ASN cc_start: 0.9196 (t0) cc_final: 0.8767 (m-40) REVERT: d 11 LEU cc_start: 0.9241 (tp) cc_final: 0.8981 (tp) REVERT: d 21 LEU cc_start: 0.8905 (tp) cc_final: 0.8530 (tp) REVERT: d 22 GLU cc_start: 0.7480 (tt0) cc_final: 0.6918 (tt0) REVERT: d 23 LEU cc_start: 0.9364 (mt) cc_final: 0.8879 (mp) REVERT: d 41 ASN cc_start: 0.8729 (m-40) cc_final: 0.8462 (m-40) REVERT: d 70 LYS cc_start: 0.8624 (tttm) cc_final: 0.8235 (ttmt) REVERT: h 39 ILE cc_start: 0.9321 (mt) cc_final: 0.9094 (tt) REVERT: h 90 ASN cc_start: 0.9123 (p0) cc_final: 0.8909 (p0) REVERT: h 96 ILE cc_start: 0.9397 (mm) cc_final: 0.8810 (mm) REVERT: j 67 MET cc_start: 0.8241 (mmt) cc_final: 0.7928 (mmp) REVERT: j 92 SER cc_start: 0.9060 (m) cc_final: 0.8264 (p) REVERT: j 95 PHE cc_start: 0.8566 (t80) cc_final: 0.7788 (t80) REVERT: j 106 LYS cc_start: 0.8823 (tttt) cc_final: 0.8591 (tptt) outliers start: 94 outliers final: 44 residues processed: 462 average time/residue: 0.1333 time to fit residues: 95.8516 Evaluate side-chains 380 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 917 ASP Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 72 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 193 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 192 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS C 180 ASN C 290 HIS ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN C 770 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN d 61 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.086656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063292 restraints weight = 71929.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.065087 restraints weight = 36921.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066255 restraints weight = 24359.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066975 restraints weight = 18893.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067424 restraints weight = 16266.744| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19870 Z= 0.225 Angle : 1.063 14.006 27788 Z= 0.475 Chirality : 0.082 1.424 3375 Planarity : 0.006 0.070 2884 Dihedral : 18.881 172.787 4198 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.91 % Rotamer: Outliers : 6.23 % Allowed : 20.23 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 1966 helix: 1.64 (0.20), residues: 712 sheet: -2.45 (0.24), residues: 325 loop : -2.35 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG g 64 TYR 0.020 0.002 TYR C 791 PHE 0.033 0.002 PHE j 24 TRP 0.031 0.002 TRP C 933 HIS 0.012 0.002 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (19870) covalent geometry : angle 1.06346 / 0.48 (27788) hydrogen bonds : bond 0.06859 / 3.48 ( 616) hydrogen bonds : angle 4.38271 / 1.73 ( 1661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 374 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.9090 (tp) cc_final: 0.8776 (tp) REVERT: A 278 ASP cc_start: 0.8098 (m-30) cc_final: 0.7573 (t0) REVERT: A 283 SER cc_start: 0.8661 (p) cc_final: 0.8336 (t) REVERT: A 331 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9195 (m-80) REVERT: A 417 TYR cc_start: 0.5907 (t80) cc_final: 0.5697 (t80) REVERT: A 529 TYR cc_start: 0.9125 (t80) cc_final: 0.8828 (t80) REVERT: A 556 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7244 (t80) REVERT: A 630 LYS cc_start: 0.9114 (tptm) cc_final: 0.7987 (tptp) REVERT: A 634 ASP cc_start: 0.8184 (m-30) cc_final: 0.6610 (m-30) REVERT: A 649 LEU cc_start: 0.9470 (tp) cc_final: 0.9211 (tp) REVERT: C 113 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8758 (mt) REVERT: C 202 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 652 MET cc_start: 0.8137 (mmm) cc_final: 0.7620 (tmm) REVERT: C 653 ASP cc_start: 0.8088 (t0) cc_final: 0.7576 (t0) REVERT: C 674 LEU cc_start: 0.8883 (mp) cc_final: 0.8637 (mp) REVERT: C 842 MET cc_start: 0.8350 (mmm) cc_final: 0.8118 (tpp) REVERT: C 968 MET cc_start: 0.8569 (mmm) cc_final: 0.8333 (mmm) REVERT: b 25 GLN cc_start: 0.9267 (mt0) cc_final: 0.8913 (mm-40) REVERT: b 28 ARG cc_start: 0.8339 (mmp80) cc_final: 0.7894 (mmp80) REVERT: b 46 ASN cc_start: 0.8463 (t0) cc_final: 0.8007 (t0) REVERT: b 47 GLU cc_start: 0.7410 (pm20) cc_final: 0.7062 (pm20) REVERT: b 50 GLU cc_start: 0.8600 (tt0) cc_final: 0.8371 (tp30) REVERT: b 85 THR cc_start: 0.9268 (p) cc_final: 0.9021 (p) REVERT: b 91 GLN cc_start: 0.9321 (mm110) cc_final: 0.9104 (mm110) REVERT: b 94 SER cc_start: 0.8775 (p) cc_final: 0.8543 (m) REVERT: b 100 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8399 (mmmt) REVERT: e 23 GLN cc_start: 0.8689 (mt0) cc_final: 0.8320 (pt0) REVERT: f 80 TYR cc_start: 0.8631 (p90) cc_final: 0.7579 (p90) REVERT: g 11 MET cc_start: 0.8184 (mmm) cc_final: 0.7982 (tpt) REVERT: g 35 PHE cc_start: 0.8656 (m-80) cc_final: 0.8370 (m-10) REVERT: g 44 MET cc_start: 0.8563 (mtt) cc_final: 0.8218 (ttm) REVERT: g 66 ASN cc_start: 0.9177 (t0) cc_final: 0.8736 (m-40) REVERT: g 72 GLU cc_start: 0.6539 (tm-30) cc_final: 0.5925 (tm-30) REVERT: d 23 LEU cc_start: 0.9413 (mt) cc_final: 0.8905 (mp) REVERT: d 37 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7547 (mt-10) REVERT: d 80 ASN cc_start: 0.8440 (m-40) cc_final: 0.8228 (m-40) REVERT: h 18 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8571 (mp0) REVERT: h 94 GLN cc_start: 0.8506 (mm110) cc_final: 0.8176 (mm-40) REVERT: j 67 MET cc_start: 0.8266 (mmt) cc_final: 0.8018 (mmm) REVERT: j 94 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8617 (tt) REVERT: j 95 PHE cc_start: 0.8599 (t80) cc_final: 0.8266 (t80) outliers start: 102 outliers final: 61 residues processed: 437 average time/residue: 0.1346 time to fit residues: 93.8874 Evaluate side-chains 385 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 556 TYR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 92 ILE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 ASN d 17 HIS h 14 GLN h 30 GLN j 51 ASN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.088646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065718 restraints weight = 71335.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067554 restraints weight = 36306.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068742 restraints weight = 23873.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069482 restraints weight = 18378.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069939 restraints weight = 15814.690| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19870 Z= 0.166 Angle : 0.990 14.612 27788 Z= 0.438 Chirality : 0.076 1.362 3375 Planarity : 0.005 0.060 2884 Dihedral : 18.514 170.934 4183 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.51 % Favored : 93.18 % Rotamer: Outliers : 5.81 % Allowed : 22.74 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1966 helix: 1.56 (0.20), residues: 713 sheet: -1.96 (0.25), residues: 350 loop : -2.34 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG g 64 TYR 0.016 0.002 TYR A 298 PHE 0.033 0.002 PHE j 24 TRP 0.030 0.002 TRP C 933 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (19870) covalent geometry : angle 0.98973 / 0.44 (27788) hydrogen bonds : bond 0.06402 / 3.24 ( 616) hydrogen bonds : angle 4.26991 / 1.69 ( 1661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 370 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9362 (tt) cc_final: 0.9132 (tt) REVERT: A 278 ASP cc_start: 0.8041 (m-30) cc_final: 0.7528 (t0) REVERT: A 331 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.9011 (m-80) REVERT: A 364 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.3468 (m-80) REVERT: A 630 LYS cc_start: 0.9161 (tptm) cc_final: 0.7867 (tptp) REVERT: A 634 ASP cc_start: 0.8148 (m-30) cc_final: 0.6545 (m-30) REVERT: C 113 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 150 MET cc_start: 0.8860 (mmm) cc_final: 0.8045 (mmt) REVERT: C 202 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: C 331 TYR cc_start: 0.8634 (m-80) cc_final: 0.8001 (m-10) REVERT: C 653 ASP cc_start: 0.8096 (t0) cc_final: 0.7489 (t0) REVERT: C 674 LEU cc_start: 0.8929 (mp) cc_final: 0.8650 (mp) REVERT: C 842 MET cc_start: 0.8395 (mmm) cc_final: 0.8176 (tpp) REVERT: C 856 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7809 (tp) REVERT: C 869 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.7788 (m90) REVERT: C 968 MET cc_start: 0.8539 (mmm) cc_final: 0.8244 (mmm) REVERT: b 28 ARG cc_start: 0.8403 (mmp80) cc_final: 0.7828 (mmp80) REVERT: b 35 MET cc_start: 0.8916 (mmm) cc_final: 0.8683 (mmm) REVERT: b 85 THR cc_start: 0.9234 (p) cc_final: 0.8950 (p) REVERT: b 94 SER cc_start: 0.8675 (p) cc_final: 0.7999 (m) REVERT: e 81 LEU cc_start: 0.8458 (tt) cc_final: 0.7800 (tp) REVERT: g 40 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5674 (pt) REVERT: g 44 MET cc_start: 0.8438 (mtt) cc_final: 0.8211 (ttm) REVERT: g 61 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6983 (p) REVERT: g 72 GLU cc_start: 0.6088 (tm-30) cc_final: 0.5879 (tm-30) REVERT: d 21 LEU cc_start: 0.8305 (tp) cc_final: 0.7881 (tp) REVERT: d 23 LEU cc_start: 0.9471 (mt) cc_final: 0.8907 (mp) REVERT: d 35 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7699 (tm-30) REVERT: d 53 GLN cc_start: 0.8819 (mp10) cc_final: 0.8500 (mm-40) REVERT: d 70 LYS cc_start: 0.9126 (ttmm) cc_final: 0.7647 (ttmm) REVERT: h 8 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8339 (ptmt) REVERT: h 18 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8514 (mp0) REVERT: h 94 GLN cc_start: 0.8298 (mm110) cc_final: 0.7591 (mm-40) REVERT: h 96 ILE cc_start: 0.9315 (mm) cc_final: 0.9050 (mm) REVERT: j 21 LEU cc_start: 0.9216 (tt) cc_final: 0.8991 (tp) REVERT: j 53 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8666 (ptpp) REVERT: j 70 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8016 (mm-30) REVERT: j 94 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8472 (tt) outliers start: 95 outliers final: 44 residues processed: 432 average time/residue: 0.1387 time to fit residues: 95.1068 Evaluate side-chains 378 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 94 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 79 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 178 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN ** d 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 HIS j 51 ASN j 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.089564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066863 restraints weight = 71812.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068739 restraints weight = 36052.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069915 restraints weight = 23478.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.070701 restraints weight = 18140.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071134 restraints weight = 15475.741| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19870 Z= 0.162 Angle : 0.971 14.719 27788 Z= 0.430 Chirality : 0.074 1.441 3375 Planarity : 0.005 0.060 2884 Dihedral : 18.296 172.759 4178 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 5.75 % Allowed : 23.66 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1966 helix: 1.42 (0.20), residues: 716 sheet: -1.80 (0.25), residues: 351 loop : -2.23 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 52 TYR 0.021 0.002 TYR g 10 PHE 0.051 0.002 PHE j 26 TRP 0.026 0.001 TRP C 933 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (19870) covalent geometry : angle 0.97124 / 0.43 (27788) hydrogen bonds : bond 0.06068 / 3.09 ( 616) hydrogen bonds : angle 4.22441 / 1.68 ( 1661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 347 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8031 (m-30) cc_final: 0.7545 (t0) REVERT: A 283 SER cc_start: 0.8533 (p) cc_final: 0.8196 (m) REVERT: A 331 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: A 364 TYR cc_start: 0.4537 (OUTLIER) cc_final: 0.3510 (m-80) REVERT: A 484 PHE cc_start: 0.7289 (t80) cc_final: 0.6985 (t80) REVERT: A 529 TYR cc_start: 0.9137 (t80) cc_final: 0.8769 (t80) REVERT: A 556 TYR cc_start: 0.6152 (t80) cc_final: 0.5798 (t80) REVERT: A 630 LYS cc_start: 0.9171 (tptm) cc_final: 0.7818 (tptp) REVERT: A 634 ASP cc_start: 0.8134 (m-30) cc_final: 0.6416 (m-30) REVERT: A 649 LEU cc_start: 0.9460 (tp) cc_final: 0.9231 (tp) REVERT: C 113 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8688 (mt) REVERT: C 126 MET cc_start: 0.9131 (tpp) cc_final: 0.8903 (tpp) REVERT: C 150 MET cc_start: 0.8725 (mmm) cc_final: 0.8163 (mmt) REVERT: C 242 VAL cc_start: 0.8535 (t) cc_final: 0.7970 (p) REVERT: C 331 TYR cc_start: 0.8548 (m-80) cc_final: 0.8012 (m-10) REVERT: C 653 ASP cc_start: 0.8439 (t0) cc_final: 0.7958 (t0) REVERT: C 674 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8632 (mp) REVERT: C 842 MET cc_start: 0.8373 (mmm) cc_final: 0.8139 (tpp) REVERT: C 869 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.7836 (m90) REVERT: b 28 ARG cc_start: 0.8573 (mmp80) cc_final: 0.8187 (mmp80) REVERT: b 35 MET cc_start: 0.8868 (mmm) cc_final: 0.8592 (mmm) REVERT: b 85 THR cc_start: 0.8960 (p) cc_final: 0.8739 (p) REVERT: f 80 TYR cc_start: 0.8576 (p90) cc_final: 0.8263 (p90) REVERT: g 10 TYR cc_start: 0.7725 (m-80) cc_final: 0.7196 (m-10) REVERT: g 24 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7662 (mmtm) REVERT: g 44 MET cc_start: 0.8473 (mtt) cc_final: 0.8223 (ttm) REVERT: g 66 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: g 72 GLU cc_start: 0.5923 (tm-30) cc_final: 0.5662 (tm-30) REVERT: d 41 ASN cc_start: 0.8605 (m-40) cc_final: 0.8272 (m110) REVERT: d 85 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7920 (mmmt) REVERT: h 18 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8807 (mt-10) REVERT: h 35 GLN cc_start: 0.9065 (mt0) cc_final: 0.8688 (pt0) REVERT: h 94 GLN cc_start: 0.8175 (mm110) cc_final: 0.7238 (mm110) REVERT: j 21 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8765 (mt) REVERT: j 31 MET cc_start: 0.8749 (tpp) cc_final: 0.8303 (tpp) REVERT: j 70 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8048 (mm-30) REVERT: j 94 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.7870 (tt) outliers start: 94 outliers final: 58 residues processed: 406 average time/residue: 0.1348 time to fit residues: 87.5746 Evaluate side-chains 384 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 92 ILE Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 171 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN A 497 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 ASN j 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.087832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065003 restraints weight = 71736.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066813 restraints weight = 36643.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067948 restraints weight = 24116.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068702 restraints weight = 18718.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069094 restraints weight = 16062.289| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19870 Z= 0.195 Angle : 0.973 14.632 27788 Z= 0.430 Chirality : 0.073 1.452 3375 Planarity : 0.005 0.060 2884 Dihedral : 18.254 174.857 4178 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.38 % Favored : 92.32 % Rotamer: Outliers : 6.42 % Allowed : 24.69 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 1966 helix: 1.29 (0.20), residues: 716 sheet: -1.81 (0.25), residues: 359 loop : -2.23 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 887 TYR 0.024 0.002 TYR g 10 PHE 0.045 0.002 PHE j 26 TRP 0.022 0.002 TRP C 933 HIS 0.004 0.001 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (19870) covalent geometry : angle 0.97334 / 0.43 (27788) hydrogen bonds : bond 0.06110 / 3.12 ( 616) hydrogen bonds : angle 4.30995 / 1.71 ( 1661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 332 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8143 (m-30) cc_final: 0.7700 (t0) REVERT: A 283 SER cc_start: 0.8576 (p) cc_final: 0.8252 (m) REVERT: A 303 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: A 331 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8932 (m-80) REVERT: A 364 TYR cc_start: 0.4579 (OUTLIER) cc_final: 0.3463 (m-80) REVERT: A 556 TYR cc_start: 0.6631 (t80) cc_final: 0.6397 (t80) REVERT: A 630 LYS cc_start: 0.9179 (tptm) cc_final: 0.7808 (tptp) REVERT: A 634 ASP cc_start: 0.8199 (m-30) cc_final: 0.6377 (m-30) REVERT: A 649 LEU cc_start: 0.9477 (tp) cc_final: 0.9254 (tp) REVERT: A 674 MET cc_start: 0.8736 (tpt) cc_final: 0.8140 (tpt) REVERT: C 113 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8666 (mt) REVERT: C 126 MET cc_start: 0.9120 (tpp) cc_final: 0.8912 (tpp) REVERT: C 242 VAL cc_start: 0.8524 (t) cc_final: 0.7968 (p) REVERT: C 331 TYR cc_start: 0.8657 (m-80) cc_final: 0.8018 (m-10) REVERT: C 500 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8053 (mmm-85) REVERT: C 653 ASP cc_start: 0.8385 (t0) cc_final: 0.7698 (t0) REVERT: C 674 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8683 (mp) REVERT: C 842 MET cc_start: 0.8391 (mmm) cc_final: 0.8133 (tpp) REVERT: C 883 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6778 (ptp90) REVERT: b 14 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8733 (p0) REVERT: b 28 ARG cc_start: 0.8611 (mmp80) cc_final: 0.8181 (mmp80) REVERT: b 52 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7783 (ttm-80) REVERT: f 74 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8338 (tpp80) REVERT: f 80 TYR cc_start: 0.8688 (p90) cc_final: 0.7495 (p90) REVERT: g 24 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7377 (mmtm) REVERT: g 35 PHE cc_start: 0.8459 (m-10) cc_final: 0.8238 (m-80) REVERT: g 44 MET cc_start: 0.8396 (mtt) cc_final: 0.8180 (ttm) REVERT: g 66 ASN cc_start: 0.9158 (t0) cc_final: 0.8611 (m-40) REVERT: d 21 LEU cc_start: 0.8377 (tp) cc_final: 0.8081 (tp) REVERT: d 35 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6844 (tm-30) REVERT: d 85 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8043 (mmmt) REVERT: h 18 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8655 (mt-10) REVERT: h 94 GLN cc_start: 0.8215 (mm110) cc_final: 0.7928 (mm110) REVERT: j 31 MET cc_start: 0.8804 (tpp) cc_final: 0.8595 (tpp) outliers start: 105 outliers final: 68 residues processed: 400 average time/residue: 0.1371 time to fit residues: 87.5064 Evaluate side-chains 390 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 92 ILE Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 84 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 64 optimal weight: 0.0670 chunk 167 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.5128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN h 14 GLN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066564 restraints weight = 72002.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068414 restraints weight = 36613.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069621 restraints weight = 23974.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070366 restraints weight = 18503.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070761 restraints weight = 15837.848| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19870 Z= 0.155 Angle : 0.952 14.969 27788 Z= 0.419 Chirality : 0.071 1.454 3375 Planarity : 0.005 0.059 2884 Dihedral : 18.187 177.155 4176 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.02 % Favored : 92.68 % Rotamer: Outliers : 5.38 % Allowed : 25.92 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 1966 helix: 1.16 (0.20), residues: 723 sheet: -1.75 (0.26), residues: 355 loop : -2.12 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 887 TYR 0.018 0.002 TYR A 417 PHE 0.055 0.002 PHE j 26 TRP 0.030 0.001 TRP C 933 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (19870) covalent geometry : angle 0.95246 / 0.42 (27788) hydrogen bonds : bond 0.05929 / 3.03 ( 616) hydrogen bonds : angle 4.22765 / 1.68 ( 1661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.9013 (tp) cc_final: 0.7765 (tp) REVERT: A 278 ASP cc_start: 0.8091 (m-30) cc_final: 0.7674 (t0) REVERT: A 283 SER cc_start: 0.8571 (p) cc_final: 0.8265 (m) REVERT: A 303 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: A 331 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: A 529 TYR cc_start: 0.9199 (t80) cc_final: 0.8818 (t80) REVERT: A 649 LEU cc_start: 0.9428 (tp) cc_final: 0.9167 (tp) REVERT: A 674 MET cc_start: 0.8691 (tpt) cc_final: 0.8108 (tpt) REVERT: C 113 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8660 (mt) REVERT: C 126 MET cc_start: 0.9137 (tpp) cc_final: 0.8868 (tpp) REVERT: C 150 MET cc_start: 0.8273 (tpp) cc_final: 0.7575 (mmt) REVERT: C 331 TYR cc_start: 0.8526 (m-80) cc_final: 0.8295 (m-80) REVERT: C 409 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8214 (t) REVERT: C 500 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8134 (mmm-85) REVERT: C 653 ASP cc_start: 0.8321 (t0) cc_final: 0.7500 (t0) REVERT: C 674 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 842 MET cc_start: 0.8301 (mmm) cc_final: 0.8052 (tpp) REVERT: C 869 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.7860 (m90) REVERT: b 5 GLN cc_start: 0.8044 (pm20) cc_final: 0.7837 (tm-30) REVERT: b 14 ASN cc_start: 0.9041 (m110) cc_final: 0.8714 (p0) REVERT: b 28 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8040 (mmp80) REVERT: b 47 GLU cc_start: 0.7534 (pm20) cc_final: 0.7257 (pm20) REVERT: b 52 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7729 (ttm-80) REVERT: e 19 ASN cc_start: 0.9384 (m-40) cc_final: 0.9030 (p0) REVERT: f 74 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8084 (ttm-80) REVERT: f 80 TYR cc_start: 0.8656 (p90) cc_final: 0.7458 (p90) REVERT: g 24 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7382 (mmtm) REVERT: g 44 MET cc_start: 0.8324 (mtt) cc_final: 0.8119 (ttm) REVERT: d 35 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6350 (tm-30) REVERT: d 85 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8033 (mmmm) REVERT: h 18 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8669 (mt-10) REVERT: h 94 GLN cc_start: 0.8078 (mm110) cc_final: 0.7219 (mm110) REVERT: j 95 PHE cc_start: 0.8279 (t80) cc_final: 0.7676 (t80) outliers start: 88 outliers final: 64 residues processed: 395 average time/residue: 0.1345 time to fit residues: 85.3763 Evaluate side-chains 385 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 313 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 92 ILE Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 51 ASN Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 71 ASN Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 134 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN h 14 GLN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.087689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064782 restraints weight = 72348.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066584 restraints weight = 37191.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067772 restraints weight = 24561.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068518 restraints weight = 18920.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068885 restraints weight = 16235.845| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19870 Z= 0.212 Angle : 0.960 14.908 27788 Z= 0.429 Chirality : 0.070 1.430 3375 Planarity : 0.005 0.060 2884 Dihedral : 18.142 178.052 4172 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.96 % Rotamer: Outliers : 5.93 % Allowed : 26.59 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1966 helix: 1.15 (0.20), residues: 723 sheet: -1.67 (0.25), residues: 376 loop : -2.11 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 64 TYR 0.022 0.002 TYR A 298 PHE 0.054 0.002 PHE j 26 TRP 0.024 0.002 TRP C 933 HIS 0.004 0.001 HIS j 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (19870) covalent geometry : angle 0.95973 / 0.43 (27788) hydrogen bonds : bond 0.06095 / 3.12 ( 616) hydrogen bonds : angle 4.36057 / 1.73 ( 1661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 318 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8177 (m-30) cc_final: 0.7682 (t0) REVERT: A 283 SER cc_start: 0.8628 (p) cc_final: 0.8351 (m) REVERT: A 303 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: A 304 ASP cc_start: 0.7506 (t0) cc_final: 0.7294 (t0) REVERT: A 331 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8986 (m-80) REVERT: A 364 TYR cc_start: 0.4140 (OUTLIER) cc_final: 0.3104 (m-80) REVERT: A 484 PHE cc_start: 0.6579 (t80) cc_final: 0.6042 (t80) REVERT: A 556 TYR cc_start: 0.5853 (t80) cc_final: 0.5585 (t80) REVERT: A 630 LYS cc_start: 0.9123 (tptm) cc_final: 0.7776 (tptp) REVERT: A 634 ASP cc_start: 0.8157 (m-30) cc_final: 0.6521 (m-30) REVERT: A 674 MET cc_start: 0.8684 (tpt) cc_final: 0.8151 (tpt) REVERT: C 113 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 150 MET cc_start: 0.8304 (tpp) cc_final: 0.7684 (mmt) REVERT: C 331 TYR cc_start: 0.8719 (m-80) cc_final: 0.8134 (m-10) REVERT: C 409 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 500 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8428 (mmm-85) REVERT: C 653 ASP cc_start: 0.8390 (t0) cc_final: 0.7753 (t0) REVERT: C 674 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 842 MET cc_start: 0.8468 (mmm) cc_final: 0.8203 (tpp) REVERT: b 14 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8758 (p0) REVERT: b 28 ARG cc_start: 0.8487 (mmp80) cc_final: 0.7934 (mmp80) REVERT: f 74 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8099 (ttm-80) REVERT: f 80 TYR cc_start: 0.8734 (p90) cc_final: 0.7508 (p90) REVERT: g 44 MET cc_start: 0.8354 (mtt) cc_final: 0.8138 (ttm) REVERT: d 21 LEU cc_start: 0.8430 (tp) cc_final: 0.8108 (tp) REVERT: d 35 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6385 (tm-30) REVERT: d 37 GLU cc_start: 0.7753 (mp0) cc_final: 0.7307 (mp0) REVERT: d 85 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8044 (mmmm) REVERT: h 18 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8826 (mt-10) REVERT: h 87 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9272 (mm) REVERT: h 94 GLN cc_start: 0.8090 (mm110) cc_final: 0.7280 (mm110) REVERT: j 31 MET cc_start: 0.8647 (tpp) cc_final: 0.8363 (tpp) REVERT: j 95 PHE cc_start: 0.8379 (t80) cc_final: 0.7785 (t80) outliers start: 97 outliers final: 75 residues processed: 374 average time/residue: 0.1326 time to fit residues: 80.0934 Evaluate side-chains 388 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 303 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 45 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 92 ILE Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN h 30 GLN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.087946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065134 restraints weight = 71732.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066936 restraints weight = 37004.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068109 restraints weight = 24522.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068776 restraints weight = 19003.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069255 restraints weight = 16413.840| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19870 Z= 0.191 Angle : 0.961 14.913 27788 Z= 0.430 Chirality : 0.069 1.398 3375 Planarity : 0.005 0.060 2884 Dihedral : 18.141 179.743 4172 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.32 % Rotamer: Outliers : 5.62 % Allowed : 27.14 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1966 helix: 1.09 (0.20), residues: 721 sheet: -1.67 (0.26), residues: 368 loop : -2.05 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG g 64 TYR 0.023 0.002 TYR C 769 PHE 0.057 0.002 PHE j 26 TRP 0.025 0.002 TRP C 933 HIS 0.006 0.001 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (19870) covalent geometry : angle 0.96145 / 0.43 (27788) hydrogen bonds : bond 0.06048 / 3.09 ( 616) hydrogen bonds : angle 4.45209 / 1.78 ( 1661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 314 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8174 (m-30) cc_final: 0.7648 (t0) REVERT: A 283 SER cc_start: 0.8665 (p) cc_final: 0.8389 (m) REVERT: A 303 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: A 331 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8981 (m-80) REVERT: A 364 TYR cc_start: 0.4145 (OUTLIER) cc_final: 0.3119 (m-80) REVERT: A 484 PHE cc_start: 0.6720 (t80) cc_final: 0.6186 (t80) REVERT: A 556 TYR cc_start: 0.6255 (t80) cc_final: 0.5954 (t80) REVERT: A 630 LYS cc_start: 0.9148 (tptm) cc_final: 0.7908 (tptp) REVERT: A 634 ASP cc_start: 0.8164 (m-30) cc_final: 0.6877 (m-30) REVERT: A 674 MET cc_start: 0.8635 (tpt) cc_final: 0.8177 (tpt) REVERT: A 689 TYR cc_start: 0.7743 (t80) cc_final: 0.7156 (t80) REVERT: C 113 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mt) REVERT: C 150 MET cc_start: 0.8373 (tpp) cc_final: 0.7854 (mmt) REVERT: C 331 TYR cc_start: 0.8694 (m-80) cc_final: 0.8106 (m-10) REVERT: C 409 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8244 (t) REVERT: C 500 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8349 (mmm-85) REVERT: C 577 LEU cc_start: 0.9119 (pp) cc_final: 0.8894 (pt) REVERT: C 653 ASP cc_start: 0.8377 (t0) cc_final: 0.7678 (t0) REVERT: C 674 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8649 (mp) REVERT: C 842 MET cc_start: 0.8443 (mmm) cc_final: 0.8177 (tpp) REVERT: b 14 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8712 (p0) REVERT: b 28 ARG cc_start: 0.8438 (mmp80) cc_final: 0.7879 (mmp80) REVERT: e 19 ASN cc_start: 0.9231 (m-40) cc_final: 0.8822 (p0) REVERT: e 81 LEU cc_start: 0.8399 (tt) cc_final: 0.7902 (tt) REVERT: f 80 TYR cc_start: 0.8693 (p90) cc_final: 0.7511 (p90) REVERT: g 44 MET cc_start: 0.8350 (mtt) cc_final: 0.8032 (mtt) REVERT: d 21 LEU cc_start: 0.8423 (tp) cc_final: 0.8065 (tp) REVERT: d 61 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7266 (tp40) REVERT: d 85 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8056 (mmmm) REVERT: h 18 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8628 (mt-10) REVERT: h 94 GLN cc_start: 0.8200 (mm110) cc_final: 0.7830 (mm110) REVERT: j 31 MET cc_start: 0.8675 (tpp) cc_final: 0.8389 (tpp) REVERT: j 95 PHE cc_start: 0.8516 (t80) cc_final: 0.8178 (t80) outliers start: 92 outliers final: 71 residues processed: 371 average time/residue: 0.1304 time to fit residues: 78.7841 Evaluate side-chains 387 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 64 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 0.0050 chunk 174 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 ASN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.090566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068395 restraints weight = 71241.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070274 restraints weight = 36416.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071482 restraints weight = 23905.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072235 restraints weight = 18391.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072626 restraints weight = 15750.345| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19870 Z= 0.161 Angle : 0.942 14.915 27788 Z= 0.420 Chirality : 0.068 1.348 3375 Planarity : 0.005 0.058 2884 Dihedral : 18.056 178.080 4171 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.32 % Rotamer: Outliers : 4.89 % Allowed : 27.81 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1966 helix: 1.00 (0.20), residues: 721 sheet: -1.58 (0.28), residues: 334 loop : -1.93 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 964 TYR 0.027 0.002 TYR C 769 PHE 0.058 0.002 PHE j 26 TRP 0.029 0.002 TRP C 933 HIS 0.006 0.001 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (19870) covalent geometry : angle 0.94201 / 0.42 (27788) hydrogen bonds : bond 0.05924 / 3.04 ( 616) hydrogen bonds : angle 4.48839 / 1.82 ( 1661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 SER cc_start: 0.8441 (p) cc_final: 0.8226 (m) REVERT: A 303 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: A 331 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8853 (m-80) REVERT: A 484 PHE cc_start: 0.6502 (t80) cc_final: 0.6163 (t80) REVERT: A 529 TYR cc_start: 0.9064 (t80) cc_final: 0.8825 (t80) REVERT: A 634 ASP cc_start: 0.7901 (m-30) cc_final: 0.7579 (m-30) REVERT: A 674 MET cc_start: 0.8493 (tpt) cc_final: 0.8064 (tpt) REVERT: C 113 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8747 (mt) REVERT: C 331 TYR cc_start: 0.8448 (m-80) cc_final: 0.8240 (m-80) REVERT: C 387 TYR cc_start: 0.8061 (m-80) cc_final: 0.7672 (m-80) REVERT: C 502 LEU cc_start: 0.9281 (tp) cc_final: 0.8996 (tt) REVERT: C 577 LEU cc_start: 0.9030 (pp) cc_final: 0.8816 (pt) REVERT: C 653 ASP cc_start: 0.7877 (t0) cc_final: 0.7422 (t0) REVERT: C 674 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8324 (mp) REVERT: b 14 ASN cc_start: 0.8885 (m110) cc_final: 0.8558 (p0) REVERT: b 18 TYR cc_start: 0.7435 (m-80) cc_final: 0.7190 (m-80) REVERT: b 28 ARG cc_start: 0.8318 (mmp80) cc_final: 0.7721 (mmp80) REVERT: e 81 LEU cc_start: 0.8266 (tt) cc_final: 0.7887 (tt) REVERT: f 80 TYR cc_start: 0.8421 (p90) cc_final: 0.7423 (p90) REVERT: d 61 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: h 18 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8490 (mt-10) REVERT: h 87 ILE cc_start: 0.9192 (mm) cc_final: 0.8931 (mm) REVERT: j 31 MET cc_start: 0.8484 (tpp) cc_final: 0.8206 (tpp) REVERT: j 95 PHE cc_start: 0.8343 (t80) cc_final: 0.8071 (t80) outliers start: 80 outliers final: 67 residues processed: 362 average time/residue: 0.1275 time to fit residues: 74.6211 Evaluate side-chains 373 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 301 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 51 ASN Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 75 LEU Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 122 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 182 optimal weight: 0.0060 chunk 174 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068306 restraints weight = 70880.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070179 restraints weight = 36511.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.071372 restraints weight = 24074.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.072109 restraints weight = 18655.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072515 restraints weight = 15994.913| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 19870 Z= 0.216 Angle : 1.048 59.199 27788 Z= 0.518 Chirality : 0.069 1.348 3375 Planarity : 0.006 0.111 2884 Dihedral : 18.065 178.082 4171 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.43 % Favored : 92.27 % Rotamer: Outliers : 5.07 % Allowed : 27.93 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1966 helix: 1.00 (0.20), residues: 721 sheet: -1.58 (0.28), residues: 334 loop : -1.92 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 41 TYR 0.028 0.002 TYR C 769 PHE 0.054 0.002 PHE j 26 TRP 0.028 0.001 TRP C 933 HIS 0.006 0.001 HIS j 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (19870) covalent geometry : angle 1.04814 / 0.52 (27788) hydrogen bonds : bond 0.05922 / 3.03 ( 616) hydrogen bonds : angle 4.49101 / 1.82 ( 1661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3872.76 seconds wall clock time: 67 minutes 47.49 seconds (4067.49 seconds total)