Starting phenix.real_space_refine on Thu Sep 18 19:12:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_8011.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_8011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_8011.map" model { file = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_8011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gam_8011/09_2025/5gam_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 4.28, per 1000 atoms: 0.22 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: 1.89 Conformation dependent library (CDL) restraints added in 802.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 3.40 Time building geometry restraints manager: 2.53 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 - 2.61: 25227 2.61 - 5.22: 2331 5.22 - 7.83: 191 7.83 - 10.44: 26 10.44 - 13.05: 13 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=" C4' C U 95 " pdb=" C3' C U 95 " pdb=" O3' C U 95 " ideal model delta sigma weight residual 109.40 122.45 -13.05 1.50e+00 4.44e-01 7.57e+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 ... (remaining 27783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 11310 35.27 - 70.55: 749 70.55 - 105.82: 69 105.82 - 141.10: 15 141.10 - 176.37: 11 Dihedral angle restraints: 12154 sinusoidal: 6234 harmonic: 5920 Sorted by residual: dihedral pdb=" CA ASN A 553 " pdb=" C ASN A 553 " pdb=" N THR A 554 " pdb=" CA THR A 554 " ideal model delta harmonic sigma weight residual 180.00 111.89 68.11 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N GLU A 465 " pdb=" CA GLU A 465 " ideal model delta harmonic sigma weight residual 180.00 124.34 55.66 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA PRO A 460 " pdb=" C PRO A 460 " pdb=" N LEU A 461 " pdb=" CA LEU A 461 " ideal model delta harmonic sigma weight residual -180.00 -129.76 -50.24 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 12151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2758 0.124 - 0.248: 543 0.248 - 0.373: 59 0.373 - 0.497: 14 0.497 - 0.621: 1 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C3' G U 129 " pdb=" C4' G U 129 " pdb=" O3' G U 129 " pdb=" C2' G U 129 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.64e+00 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 -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.46e+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: 5.450 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 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= 0.556 Angle : 1.490 13.051 27788 Z= 1.027 Chirality : 0.099 0.621 3375 Planarity : 0.008 0.143 2884 Dihedral : 22.022 176.373 8312 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 aren 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 covalent geometry : bond 0.00798 (19870) covalent geometry : angle 1.48963 (27788) hydrogen bonds : bond 0.13956 ( 616) hydrogen bonds : angle 6.25736 ( 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 : 0.653 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: 0.7660 (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: 0.8662 (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: 0.8913 (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: 0.1427 time to fit residues: 133.9317 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 : 1.015 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 216 GLN A 310 ASN A 326 ASN 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 77 ASN d 41 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 94 GLN j 28 HIS j 52 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.086962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063583 restraints weight = 71870.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065421 restraints weight = 36741.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066580 restraints weight = 24108.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067330 restraints weight = 18689.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067773 restraints weight = 16028.468| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19870 Z= 0.241 Angle : 0.906 14.216 27788 Z= 0.462 Chirality : 0.053 0.385 3375 Planarity : 0.007 0.091 2884 Dihedral : 23.364 179.211 4809 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.03 % Rotamer: Outliers : 5.93 % Allowed : 18.46 % Favored : 75.61 % 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 aren not related in a simple way. whole: -1.49 (0.19), residues: 1966 helix: 1.90 (0.20), residues: 706 sheet: -2.69 (0.24), residues: 308 loop : -2.79 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 64 TYR 0.034 0.002 TYR C 791 PHE 0.027 0.002 PHE A 506 TRP 0.044 0.002 TRP C 933 HIS 0.009 0.001 HIS j 28 Details of bonding type rmsd covalent geometry : bond 0.00527 (19870) covalent geometry : angle 0.90630 (27788) hydrogen bonds : bond 0.07383 ( 616) hydrogen bonds : angle 4.40214 ( 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 496 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 399 time to evaluate : 0.533 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: 0.9172 (tp) cc_final: 0.8772 (tp) REVERT: A 228 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8543 (tptt) REVERT: A 278 ASP cc_start: 0.8001 (m-30) cc_final: 0.7550 (t0) REVERT: A 417 TYR cc_start: 0.5854 (t80) cc_final: 0.5576 (t80) REVERT: A 493 MET cc_start: 0.8170 (mtt) cc_final: 0.7742 (mtt) REVERT: A 529 TYR cc_start: 0.9120 (t80) cc_final: 0.8843 (t80) REVERT: A 558 GLN cc_start: 0.8537 (mp10) cc_final: 0.8053 (mp10) REVERT: A 630 LYS cc_start: 0.8943 (tptm) cc_final: 0.8010 (tptp) REVERT: A 631 LEU cc_start: 0.9352 (mt) cc_final: 0.9121 (mt) REVERT: A 634 ASP cc_start: 0.8195 (m-30) cc_final: 0.7068 (m-30) REVERT: C 113 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8719 (mt) REVERT: C 202 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: C 264 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.6528 (m) REVERT: C 331 TYR cc_start: 0.8625 (m-80) cc_final: 0.7677 (m-10) REVERT: C 387 TYR cc_start: 0.8173 (m-80) cc_final: 0.7355 (m-80) REVERT: C 409 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8280 (t) REVERT: C 439 ILE cc_start: 0.9138 (mt) cc_final: 0.8887 (mt) REVERT: C 502 LEU cc_start: 0.9017 (mt) cc_final: 0.8626 (mt) REVERT: C 653 ASP cc_start: 0.7905 (t0) cc_final: 0.7645 (t0) REVERT: C 658 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8048 (t0) REVERT: C 674 LEU cc_start: 0.8687 (mp) cc_final: 0.8466 (mp) REVERT: C 842 MET cc_start: 0.8321 (mmm) cc_final: 0.8020 (tpp) REVERT: C 962 LEU cc_start: 0.8671 (tp) cc_final: 0.8435 (tp) REVERT: C 968 MET cc_start: 0.8488 (mmm) cc_final: 0.8280 (mmm) REVERT: b 18 TYR cc_start: 0.7572 (m-80) cc_final: 0.6968 (m-80) REVERT: b 33 GLN cc_start: 0.8050 (mp10) cc_final: 0.7552 (mm-40) REVERT: b 46 ASN cc_start: 0.8920 (t0) cc_final: 0.8118 (t0) REVERT: b 91 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8804 (mp10) REVERT: b 94 SER cc_start: 0.8976 (p) cc_final: 0.8404 (m) REVERT: e 23 GLN cc_start: 0.8677 (mt0) cc_final: 0.8288 (pt0) REVERT: f 80 TYR cc_start: 0.8532 (p90) cc_final: 0.7567 (p90) REVERT: g 11 MET cc_start: 0.7610 (mmm) cc_final: 0.7250 (tpt) REVERT: d 21 LEU cc_start: 0.8880 (tp) cc_final: 0.8501 (tp) REVERT: d 22 GLU cc_start: 0.7468 (tt0) cc_final: 0.7022 (tt0) REVERT: d 23 LEU cc_start: 0.9356 (mt) cc_final: 0.8889 (mp) REVERT: d 35 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7621 (tm-30) REVERT: d 41 ASN cc_start: 0.8701 (m-40) cc_final: 0.8305 (m-40) REVERT: d 70 LYS cc_start: 0.8658 (tttm) cc_final: 0.8328 (ttmt) REVERT: d 80 ASN cc_start: 0.8434 (m-40) cc_final: 0.7963 (m-40) REVERT: h 4 VAL cc_start: 0.9608 (t) cc_final: 0.9402 (p) REVERT: h 39 ILE cc_start: 0.9329 (mt) cc_final: 0.9109 (tt) REVERT: h 96 ILE cc_start: 0.9420 (mm) cc_final: 0.8831 (mm) REVERT: j 18 LEU cc_start: 0.6425 (mt) cc_final: 0.6170 (mp) REVERT: j 67 MET cc_start: 0.8197 (mmt) cc_final: 0.7846 (mmp) REVERT: j 92 SER cc_start: 0.9057 (m) cc_final: 0.8263 (p) REVERT: j 106 LYS cc_start: 0.8844 (tttt) cc_final: 0.8618 (tptt) outliers start: 97 outliers final: 45 residues processed: 463 average time/residue: 0.1271 time to fit residues: 90.8262 Evaluate side-chains 372 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 228 LYS 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 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 260 ASN 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 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 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 39 ILE 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: 6.9990 chunk 188 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 54 ASN ** 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 ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.085796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062612 restraints weight = 72925.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064401 restraints weight = 37235.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065546 restraints weight = 24502.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066265 restraints weight = 18978.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066633 restraints weight = 16306.311| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19870 Z= 0.235 Angle : 0.848 13.896 27788 Z= 0.432 Chirality : 0.051 0.336 3375 Planarity : 0.006 0.069 2884 Dihedral : 23.075 175.755 4764 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.04 % Favored : 91.61 % Rotamer: Outliers : 6.11 % Allowed : 21.09 % Favored : 72.80 % 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 aren not related in a simple way. whole: -1.35 (0.19), residues: 1966 helix: 1.68 (0.20), residues: 706 sheet: -2.52 (0.24), residues: 321 loop : -2.41 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 52 TYR 0.022 0.002 TYR C 791 PHE 0.034 0.002 PHE j 24 TRP 0.032 0.002 TRP C 933 HIS 0.012 0.001 HIS j 28 Details of bonding type rmsd covalent geometry : bond 0.00515 (19870) covalent geometry : angle 0.84833 (27788) hydrogen bonds : bond 0.06742 ( 616) hydrogen bonds : angle 4.40283 ( 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 462 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 362 time to evaluate : 0.694 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: 0.9080 (tp) cc_final: 0.8755 (tp) REVERT: A 278 ASP cc_start: 0.8128 (m-30) cc_final: 0.7572 (t0) REVERT: A 417 TYR cc_start: 0.5937 (t80) cc_final: 0.5726 (t80) REVERT: A 529 TYR cc_start: 0.9109 (t80) cc_final: 0.8852 (t80) REVERT: A 556 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7282 (t80) REVERT: A 630 LYS cc_start: 0.9071 (tptm) cc_final: 0.7900 (tptp) REVERT: A 634 ASP cc_start: 0.8230 (m-30) cc_final: 0.6607 (m-30) REVERT: A 649 LEU cc_start: 0.9513 (tp) cc_final: 0.9234 (tp) REVERT: C 113 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 150 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7932 (mmt) REVERT: C 652 MET cc_start: 0.8180 (mmm) cc_final: 0.7899 (tmm) REVERT: C 653 ASP cc_start: 0.8133 (t0) cc_final: 0.7641 (t0) REVERT: C 674 LEU cc_start: 0.8918 (mp) cc_final: 0.8690 (mp) REVERT: C 720 ILE cc_start: 0.9201 (mt) cc_final: 0.8947 (tp) REVERT: C 842 MET cc_start: 0.8422 (mmm) cc_final: 0.8216 (tpt) REVERT: C 968 MET cc_start: 0.8587 (mmm) cc_final: 0.8352 (mmm) REVERT: b 18 TYR cc_start: 0.7635 (m-80) cc_final: 0.7431 (m-80) REVERT: b 25 GLN cc_start: 0.9321 (mm-40) cc_final: 0.9119 (mm-40) REVERT: b 28 ARG cc_start: 0.8381 (mmp80) cc_final: 0.7688 (mmp80) REVERT: b 50 GLU cc_start: 0.8668 (tt0) cc_final: 0.8360 (tp30) REVERT: b 85 THR cc_start: 0.9284 (p) cc_final: 0.9052 (p) REVERT: b 91 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8782 (mp10) REVERT: e 23 GLN cc_start: 0.8726 (mt0) cc_final: 0.8337 (pt0) REVERT: e 80 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6885 (mm) REVERT: f 68 LEU cc_start: 0.8438 (mm) cc_final: 0.8160 (mm) REVERT: f 80 TYR cc_start: 0.8956 (p90) cc_final: 0.8593 (p90) REVERT: g 11 MET cc_start: 0.8224 (mmm) cc_final: 0.7992 (tpt) REVERT: g 44 MET cc_start: 0.8523 (mtt) cc_final: 0.8200 (ttm) REVERT: g 66 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: g 72 GLU cc_start: 0.6553 (tm-30) cc_final: 0.6189 (tm-30) REVERT: d 23 LEU cc_start: 0.9408 (mt) cc_final: 0.8741 (mp) REVERT: d 37 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7409 (mt-10) REVERT: d 41 ASN cc_start: 0.8931 (m-40) cc_final: 0.8687 (m110) REVERT: d 70 LYS cc_start: 0.8673 (tttm) cc_final: 0.8181 (ttmt) REVERT: h 4 VAL cc_start: 0.9447 (t) cc_final: 0.9238 (p) REVERT: h 18 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8727 (pt0) REVERT: h 30 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8153 (mm-40) REVERT: j 53 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8634 (pttm) REVERT: j 67 MET cc_start: 0.8132 (mmt) cc_final: 0.7763 (mmm) REVERT: j 92 SER cc_start: 0.9154 (m) cc_final: 0.8938 (p) outliers start: 100 outliers final: 59 residues processed: 423 average time/residue: 0.1281 time to fit residues: 86.0740 Evaluate side-chains 378 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 150 MET 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 260 ASN Chi-restraints excluded: chain C residue 361 THR 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 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 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 55 ASP Chi-restraints excluded: chain e residue 80 ILE 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 66 ASN Chi-restraints excluded: chain g residue 71 LEU 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 25 VAL Chi-restraints excluded: chain h residue 30 GLN 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 j residue 34 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 20 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** 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 33 GLN ** f 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 ASN d 17 HIS d 80 ASN h 30 GLN j 35 ASN j 51 ASN j 66 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.088459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066103 restraints weight = 71425.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067961 restraints weight = 36116.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069125 restraints weight = 23608.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069864 restraints weight = 18249.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.070216 restraints weight = 15685.492| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19870 Z= 0.163 Angle : 0.802 14.240 27788 Z= 0.402 Chirality : 0.049 0.321 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.822 173.806 4754 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.61 % Favored : 93.08 % Rotamer: Outliers : 5.56 % Allowed : 22.98 % 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 aren not related in a simple way. whole: -1.28 (0.19), residues: 1966 helix: 1.45 (0.20), residues: 716 sheet: -2.12 (0.24), residues: 339 loop : -2.30 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 52 TYR 0.018 0.002 TYR A 391 PHE 0.030 0.002 PHE j 24 TRP 0.029 0.002 TRP C 933 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00364 (19870) covalent geometry : angle 0.80186 (27788) hydrogen bonds : bond 0.06116 ( 616) hydrogen bonds : angle 4.21426 ( 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 450 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 359 time to evaluate : 0.697 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 175 LEU cc_start: 0.9310 (tt) cc_final: 0.9101 (tt) REVERT: A 278 ASP cc_start: 0.7810 (m-30) cc_final: 0.7393 (t0) REVERT: A 364 TYR cc_start: 0.4525 (OUTLIER) cc_final: 0.3611 (m-80) REVERT: A 529 TYR cc_start: 0.9050 (t80) cc_final: 0.8790 (t80) REVERT: A 630 LYS cc_start: 0.9121 (tptm) cc_final: 0.7826 (tptp) REVERT: A 634 ASP cc_start: 0.7944 (m-30) cc_final: 0.6255 (m-30) REVERT: C 113 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8738 (mt) REVERT: C 150 MET cc_start: 0.8234 (tpp) cc_final: 0.7622 (mmt) REVERT: C 309 ASN cc_start: 0.8079 (m-40) cc_final: 0.7639 (t0) REVERT: C 331 TYR cc_start: 0.8565 (m-80) cc_final: 0.7824 (m-10) REVERT: C 653 ASP cc_start: 0.7828 (t0) cc_final: 0.7207 (t0) REVERT: C 674 LEU cc_start: 0.8744 (mp) cc_final: 0.8478 (mp) REVERT: C 856 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7721 (tp) REVERT: C 869 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.7808 (m90) REVERT: b 18 TYR cc_start: 0.7848 (m-80) cc_final: 0.7449 (m-80) REVERT: b 25 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9076 (mm-40) REVERT: b 28 ARG cc_start: 0.8349 (mmp80) cc_final: 0.8139 (mmp80) REVERT: b 91 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8745 (mp10) REVERT: e 81 LEU cc_start: 0.8862 (tt) cc_final: 0.8520 (tp) REVERT: g 10 TYR cc_start: 0.8149 (m-80) cc_final: 0.7847 (m-10) REVERT: g 40 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5733 (pt) REVERT: g 61 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6859 (p) REVERT: g 64 ARG cc_start: 0.8679 (ttt90) cc_final: 0.8459 (ttt90) REVERT: g 72 GLU cc_start: 0.6421 (tm-30) cc_final: 0.6076 (tm-30) REVERT: d 21 LEU cc_start: 0.8519 (tp) cc_final: 0.8025 (tp) REVERT: d 22 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6506 (tm-30) REVERT: d 23 LEU cc_start: 0.9239 (mt) cc_final: 0.8473 (mp) REVERT: d 37 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7191 (mt-10) REVERT: d 41 ASN cc_start: 0.8995 (m-40) cc_final: 0.8755 (m110) REVERT: h 4 VAL cc_start: 0.9332 (t) cc_final: 0.9131 (p) REVERT: h 18 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8638 (mt-10) REVERT: j 21 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8666 (mt) REVERT: j 67 MET cc_start: 0.8075 (mmt) cc_final: 0.7404 (mmm) REVERT: j 92 SER cc_start: 0.9109 (m) cc_final: 0.8790 (p) REVERT: j 95 PHE cc_start: 0.8301 (t80) cc_final: 0.7136 (t80) outliers start: 91 outliers final: 50 residues processed: 418 average time/residue: 0.1201 time to fit residues: 80.2045 Evaluate side-chains 378 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 364 TYR 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 193 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 219 VAL 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 381 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 916 THR 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 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 92 ILE 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 40 LEU 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 76 ASP Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 94 optimal weight: 0.9990 chunk 125 optimal weight: 0.0570 chunk 79 optimal weight: 0.0060 chunk 26 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 203 ASN A 658 ASN C 180 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** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.089440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067450 restraints weight = 71366.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069307 restraints weight = 35805.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070503 restraints weight = 23309.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.071243 restraints weight = 17899.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.071706 restraints weight = 15330.957| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19870 Z= 0.147 Angle : 0.783 14.400 27788 Z= 0.391 Chirality : 0.048 0.313 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.545 173.762 4749 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.66 % Favored : 93.03 % Rotamer: Outliers : 5.44 % Allowed : 24.76 % Favored : 69.80 % 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 aren not related in a simple way. whole: -1.36 (0.19), residues: 1966 helix: 1.20 (0.20), residues: 726 sheet: -2.05 (0.24), residues: 375 loop : -2.24 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 52 TYR 0.029 0.002 TYR h 84 PHE 0.049 0.002 PHE j 26 TRP 0.031 0.001 TRP C 933 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00320 (19870) covalent geometry : angle 0.78292 (27788) hydrogen bonds : bond 0.05749 ( 616) hydrogen bonds : angle 4.15401 ( 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 439 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 350 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.7771 (m-30) cc_final: 0.7378 (t0) REVERT: A 303 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: A 364 TYR cc_start: 0.4715 (OUTLIER) cc_final: 0.3650 (m-80) REVERT: A 529 TYR cc_start: 0.9073 (t80) cc_final: 0.8811 (t80) REVERT: A 649 LEU cc_start: 0.9407 (tp) cc_final: 0.9181 (tp) REVERT: C 113 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 150 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7525 (mmt) REVERT: C 242 VAL cc_start: 0.8426 (t) cc_final: 0.7894 (p) REVERT: C 653 ASP cc_start: 0.8060 (t0) cc_final: 0.7611 (t0) REVERT: C 674 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 842 MET cc_start: 0.7420 (tpp) cc_final: 0.7071 (tpp) REVERT: C 869 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.7807 (m90) REVERT: b 18 TYR cc_start: 0.7779 (m-80) cc_final: 0.7523 (m-80) REVERT: b 28 ARG cc_start: 0.8387 (mmp80) cc_final: 0.8142 (mmp80) REVERT: b 91 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8603 (mp10) REVERT: g 10 TYR cc_start: 0.8072 (m-80) cc_final: 0.7746 (m-10) REVERT: g 40 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5820 (pt) REVERT: g 44 MET cc_start: 0.8310 (ttm) cc_final: 0.7975 (ttm) REVERT: g 61 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6811 (p) REVERT: g 72 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6124 (tm-30) REVERT: d 23 LEU cc_start: 0.9261 (mt) cc_final: 0.8952 (mp) REVERT: d 37 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7143 (mt-10) REVERT: d 53 GLN cc_start: 0.8791 (mp10) cc_final: 0.8390 (mp10) REVERT: d 68 GLN cc_start: 0.8691 (mm-40) cc_final: 0.7960 (mm110) REVERT: h 9 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8163 (mtmm) REVERT: h 35 GLN cc_start: 0.8993 (mt0) cc_final: 0.8779 (pt0) REVERT: h 87 ILE cc_start: 0.9358 (mm) cc_final: 0.9151 (mm) REVERT: h 92 ILE cc_start: 0.7275 (pt) cc_final: 0.7035 (pt) REVERT: h 94 GLN cc_start: 0.8250 (mm110) cc_final: 0.7877 (mm110) REVERT: j 21 LEU cc_start: 0.8902 (tt) cc_final: 0.8525 (mt) REVERT: j 31 MET cc_start: 0.8452 (tpp) cc_final: 0.8149 (tpp) REVERT: j 92 SER cc_start: 0.9173 (m) cc_final: 0.8866 (p) REVERT: j 95 PHE cc_start: 0.8157 (t80) cc_final: 0.7696 (t80) outliers start: 89 outliers final: 51 residues processed: 403 average time/residue: 0.1197 time to fit residues: 76.6631 Evaluate side-chains 375 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 303 PHE Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 548 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 150 MET Chi-restraints excluded: chain C residue 157 SER 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 264 CYS Chi-restraints excluded: chain C residue 361 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 574 SER 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 773 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL 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 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 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 63 VAL Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR 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 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 84 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 171 optimal weight: 6.9990 chunk 197 optimal weight: 0.0020 chunk 77 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN A 559 GLN C 180 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.087685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065325 restraints weight = 71197.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067148 restraints weight = 36132.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068298 restraints weight = 23753.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069053 restraints weight = 18478.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069483 restraints weight = 15823.718| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5057 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= 0.212 Angle : 0.808 14.615 27788 Z= 0.402 Chirality : 0.049 0.378 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.404 172.732 4749 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.58 % Favored : 92.07 % Rotamer: Outliers : 5.93 % Allowed : 25.55 % Favored : 68.52 % 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 aren not related in a simple way. whole: -1.31 (0.19), residues: 1966 helix: 1.20 (0.20), residues: 722 sheet: -1.82 (0.25), residues: 370 loop : -2.27 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 52 TYR 0.024 0.002 TYR A 298 PHE 0.029 0.002 PHE d 63 TRP 0.028 0.002 TRP C 933 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00475 (19870) covalent geometry : angle 0.80760 (27788) hydrogen bonds : bond 0.05881 ( 616) hydrogen bonds : angle 4.32771 ( 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 417 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 320 time to evaluate : 0.656 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 278 ASP cc_start: 0.7998 (m-30) cc_final: 0.7608 (t0) REVERT: A 283 SER cc_start: 0.8567 (p) cc_final: 0.8290 (m) REVERT: A 364 TYR cc_start: 0.4323 (OUTLIER) cc_final: 0.3202 (m-80) REVERT: A 529 TYR cc_start: 0.9136 (t80) cc_final: 0.8908 (t80) REVERT: A 649 LEU cc_start: 0.9453 (tp) cc_final: 0.9246 (tp) REVERT: A 674 MET cc_start: 0.8665 (tpt) cc_final: 0.8127 (tpt) REVERT: A 701 CYS cc_start: 0.6943 (t) cc_final: 0.6700 (t) REVERT: C 113 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8785 (mt) REVERT: C 150 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7643 (mmt) REVERT: C 242 VAL cc_start: 0.8504 (t) cc_final: 0.7964 (p) REVERT: C 458 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (pt) REVERT: C 593 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: C 653 ASP cc_start: 0.8207 (t0) cc_final: 0.7717 (t0) REVERT: C 674 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8355 (mp) REVERT: C 842 MET cc_start: 0.7731 (tpp) cc_final: 0.7365 (tpp) REVERT: b 18 TYR cc_start: 0.8002 (m-80) cc_final: 0.7793 (m-80) REVERT: b 23 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8513 (mt) REVERT: b 25 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8957 (mm-40) REVERT: b 28 ARG cc_start: 0.8493 (mmp80) cc_final: 0.8167 (mmp80) REVERT: b 31 ILE cc_start: 0.8181 (mm) cc_final: 0.7781 (mm) REVERT: g 10 TYR cc_start: 0.8432 (m-80) cc_final: 0.7881 (m-10) REVERT: d 23 LEU cc_start: 0.9180 (mt) cc_final: 0.8935 (mp) REVERT: d 53 GLN cc_start: 0.8871 (mp10) cc_final: 0.8356 (mp10) REVERT: j 21 LEU cc_start: 0.8904 (tt) cc_final: 0.8486 (mt) REVERT: j 57 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: j 92 SER cc_start: 0.9196 (m) cc_final: 0.8861 (p) REVERT: j 93 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.6972 (mttt) outliers start: 97 outliers final: 66 residues processed: 382 average time/residue: 0.1255 time to fit residues: 75.4807 Evaluate side-chains 371 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 560 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 168 VAL 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 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 458 ILE 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 574 SER Chi-restraints excluded: chain C residue 593 LYS 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 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL 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 23 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 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 63 VAL 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 57 THR 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 32 VAL 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 84 VAL Chi-restraints excluded: chain j residue 93 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 64 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 160 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 GLN j 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.088646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066535 restraints weight = 71598.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068395 restraints weight = 36266.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069572 restraints weight = 23756.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070209 restraints weight = 18392.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070724 restraints weight = 15961.119| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19870 Z= 0.169 Angle : 0.796 14.877 27788 Z= 0.394 Chirality : 0.048 0.351 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.203 172.201 4747 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.02 % Favored : 92.68 % Rotamer: Outliers : 5.44 % Allowed : 26.83 % Favored : 67.73 % 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 aren not related in a simple way. whole: -1.32 (0.19), residues: 1966 helix: 1.13 (0.20), residues: 719 sheet: -2.00 (0.26), residues: 354 loop : -2.11 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 964 TYR 0.027 0.002 TYR C 331 PHE 0.037 0.002 PHE j 24 TRP 0.028 0.001 TRP C 933 HIS 0.008 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00380 (19870) covalent geometry : angle 0.79570 (27788) hydrogen bonds : bond 0.05716 ( 616) hydrogen bonds : angle 4.24186 ( 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 416 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 327 time to evaluate : 0.505 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 278 ASP cc_start: 0.7938 (m-30) cc_final: 0.7521 (t0) REVERT: A 283 SER cc_start: 0.8504 (p) cc_final: 0.8237 (m) REVERT: A 303 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: A 364 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.3341 (m-80) REVERT: A 529 TYR cc_start: 0.9147 (t80) cc_final: 0.8925 (t80) REVERT: A 630 LYS cc_start: 0.9111 (tptm) cc_final: 0.7718 (tptp) REVERT: A 634 ASP cc_start: 0.7969 (m-30) cc_final: 0.6333 (m-30) REVERT: A 649 LEU cc_start: 0.9405 (tp) cc_final: 0.9184 (tp) REVERT: A 674 MET cc_start: 0.8648 (tpt) cc_final: 0.8139 (tpt) REVERT: A 701 CYS cc_start: 0.7092 (t) cc_final: 0.6845 (t) REVERT: C 113 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8665 (mt) REVERT: C 150 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7602 (mmt) REVERT: C 202 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: C 331 TYR cc_start: 0.8352 (m-10) cc_final: 0.7744 (m-10) REVERT: C 653 ASP cc_start: 0.8146 (t0) cc_final: 0.7665 (t0) REVERT: C 674 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 842 MET cc_start: 0.7710 (tpp) cc_final: 0.7288 (tpp) REVERT: b 18 TYR cc_start: 0.7914 (m-80) cc_final: 0.7697 (m-80) REVERT: b 28 ARG cc_start: 0.8567 (mmp80) cc_final: 0.8215 (mmp80) REVERT: b 47 GLU cc_start: 0.7376 (pm20) cc_final: 0.7157 (pm20) REVERT: b 52 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7259 (ttm-80) REVERT: e 19 ASN cc_start: 0.9322 (m-40) cc_final: 0.9091 (p0) REVERT: g 10 TYR cc_start: 0.8382 (m-80) cc_final: 0.8142 (m-10) REVERT: g 24 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7799 (mmtm) REVERT: d 68 GLN cc_start: 0.8800 (mm-40) cc_final: 0.7906 (mm-40) REVERT: j 92 SER cc_start: 0.9229 (m) cc_final: 0.8903 (p) REVERT: j 95 PHE cc_start: 0.7772 (t80) cc_final: 0.7514 (t80) outliers start: 89 outliers final: 60 residues processed: 379 average time/residue: 0.1264 time to fit residues: 76.1801 Evaluate side-chains 367 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 301 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 364 TYR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 150 MET 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 259 ASN 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 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 501 ILE Chi-restraints excluded: chain C residue 574 SER 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 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 908 VAL Chi-restraints excluded: chain C residue 916 THR 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 92 ILE 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 73 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 21 LEU Chi-restraints excluded: chain d residue 57 THR 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 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 51 ASN Chi-restraints excluded: chain j residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 134 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 0.0170 chunk 95 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.089313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067187 restraints weight = 72425.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069063 restraints weight = 36447.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.070270 restraints weight = 23777.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071015 restraints weight = 18309.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071461 restraints weight = 15688.700| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19870 Z= 0.155 Angle : 0.804 14.985 27788 Z= 0.396 Chirality : 0.048 0.339 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.070 172.615 4745 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.22 % Favored : 92.52 % Rotamer: Outliers : 4.58 % Allowed : 28.00 % Favored : 67.42 % 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 aren not related in a simple way. whole: -1.21 (0.19), residues: 1966 helix: 1.17 (0.20), residues: 720 sheet: -1.91 (0.26), residues: 353 loop : -2.02 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 30 TYR 0.025 0.002 TYR A 556 PHE 0.031 0.002 PHE d 63 TRP 0.030 0.001 TRP C 933 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00347 (19870) covalent geometry : angle 0.80423 (27788) hydrogen bonds : bond 0.05589 ( 616) hydrogen bonds : angle 4.21063 ( 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 392 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 0.531 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 175 LEU cc_start: 0.9387 (tt) cc_final: 0.9135 (tt) REVERT: A 278 ASP cc_start: 0.7918 (m-30) cc_final: 0.7534 (t0) REVERT: A 283 SER cc_start: 0.8470 (p) cc_final: 0.8207 (m) REVERT: A 303 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 364 TYR cc_start: 0.4578 (OUTLIER) cc_final: 0.3272 (m-80) REVERT: A 529 TYR cc_start: 0.9146 (t80) cc_final: 0.8926 (t80) REVERT: A 556 TYR cc_start: 0.5865 (t80) cc_final: 0.5375 (t80) REVERT: A 630 LYS cc_start: 0.9136 (tptm) cc_final: 0.7746 (tptp) REVERT: A 634 ASP cc_start: 0.7882 (m-30) cc_final: 0.6238 (m-30) REVERT: A 649 LEU cc_start: 0.9374 (tp) cc_final: 0.9142 (tp) REVERT: A 674 MET cc_start: 0.8610 (tpt) cc_final: 0.8127 (tpt) REVERT: C 113 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8688 (mt) REVERT: C 150 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7603 (mmt) REVERT: C 210 ILE cc_start: 0.9453 (mm) cc_final: 0.9206 (mm) REVERT: C 331 TYR cc_start: 0.8080 (m-10) cc_final: 0.7783 (m-10) REVERT: C 653 ASP cc_start: 0.7797 (t0) cc_final: 0.7443 (t0) REVERT: C 674 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8282 (mp) REVERT: C 842 MET cc_start: 0.7669 (tpp) cc_final: 0.7323 (tpp) REVERT: b 17 ASP cc_start: 0.8368 (t0) cc_final: 0.7679 (t0) REVERT: b 18 TYR cc_start: 0.8017 (m-80) cc_final: 0.7672 (m-80) REVERT: b 19 LYS cc_start: 0.8222 (tptp) cc_final: 0.8004 (tptp) REVERT: b 28 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8082 (mmp80) REVERT: e 19 ASN cc_start: 0.9368 (m-40) cc_final: 0.9066 (p0) REVERT: g 35 PHE cc_start: 0.8257 (m-10) cc_final: 0.8052 (m-80) REVERT: d 68 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8061 (mm-40) REVERT: j 92 SER cc_start: 0.9236 (m) cc_final: 0.8898 (p) REVERT: j 95 PHE cc_start: 0.8040 (t80) cc_final: 0.7691 (t80) outliers start: 75 outliers final: 57 residues processed: 361 average time/residue: 0.1259 time to fit residues: 72.0732 Evaluate side-chains 359 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 297 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU 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 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 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 259 ASN 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 432 GLN 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 501 ILE Chi-restraints excluded: chain C residue 574 SER 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 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 908 VAL Chi-restraints excluded: chain C residue 916 THR 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 53 VAL Chi-restraints excluded: chain b residue 92 ILE 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 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 57 THR 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 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 71 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS ** f 77 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.088330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066095 restraints weight = 72173.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067952 restraints weight = 36683.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069113 restraints weight = 24074.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069849 restraints weight = 18661.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070274 restraints weight = 16062.575| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19870 Z= 0.187 Angle : 0.816 14.915 27788 Z= 0.402 Chirality : 0.048 0.299 3375 Planarity : 0.005 0.060 2884 Dihedral : 22.025 172.149 4744 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 4.77 % Allowed : 28.06 % Favored : 67.18 % 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 aren not related in a simple way. whole: -1.20 (0.19), residues: 1966 helix: 1.16 (0.20), residues: 722 sheet: -1.82 (0.26), residues: 358 loop : -2.04 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG j 41 TYR 0.029 0.002 TYR A 417 PHE 0.035 0.002 PHE j 24 TRP 0.027 0.002 TRP C 933 HIS 0.011 0.001 HIS b 40 Details of bonding type rmsd covalent geometry : bond 0.00419 (19870) covalent geometry : angle 0.81625 (27788) hydrogen bonds : bond 0.05684 ( 616) hydrogen bonds : angle 4.32822 ( 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 385 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8059 (mpp) cc_final: 0.7762 (ptp) REVERT: A 175 LEU cc_start: 0.9413 (tt) cc_final: 0.9160 (tt) REVERT: A 283 SER cc_start: 0.8529 (p) cc_final: 0.8280 (m) REVERT: A 303 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 364 TYR cc_start: 0.4447 (OUTLIER) cc_final: 0.3297 (m-80) REVERT: A 529 TYR cc_start: 0.9166 (t80) cc_final: 0.8946 (t80) REVERT: A 533 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7724 (tp30) REVERT: A 630 LYS cc_start: 0.9161 (tptm) cc_final: 0.7777 (tptp) REVERT: A 634 ASP cc_start: 0.7920 (m-30) cc_final: 0.6263 (m-30) REVERT: A 649 LEU cc_start: 0.9431 (tp) cc_final: 0.9177 (tp) REVERT: A 674 MET cc_start: 0.8602 (tpt) cc_final: 0.8134 (tpt) REVERT: A 701 CYS cc_start: 0.7869 (t) cc_final: 0.7447 (t) REVERT: C 113 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 150 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7668 (mmt) REVERT: C 502 LEU cc_start: 0.9247 (tp) cc_final: 0.9046 (tt) REVERT: C 653 ASP cc_start: 0.7891 (t0) cc_final: 0.7677 (t0) REVERT: C 674 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 842 MET cc_start: 0.7720 (tpp) cc_final: 0.7355 (tpp) REVERT: b 18 TYR cc_start: 0.8007 (m-80) cc_final: 0.7779 (m-80) REVERT: b 28 ARG cc_start: 0.8529 (mmp80) cc_final: 0.8230 (mmp80) REVERT: e 19 ASN cc_start: 0.9396 (m-40) cc_final: 0.9193 (m-40) REVERT: d 68 GLN cc_start: 0.8813 (mm-40) cc_final: 0.7908 (mm-40) REVERT: j 92 SER cc_start: 0.9255 (m) cc_final: 0.8879 (p) REVERT: j 93 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7132 (mttt) outliers start: 78 outliers final: 62 residues processed: 352 average time/residue: 0.1185 time to fit residues: 67.1671 Evaluate side-chains 360 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 615 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 168 VAL 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 432 GLN 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 501 ILE Chi-restraints excluded: chain C residue 574 SER 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 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 908 VAL 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 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 53 VAL 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 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 57 THR 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 32 VAL 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 51 ASN Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 93 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 64 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 174 optimal weight: 0.0970 chunk 151 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 90 optimal weight: 0.1980 chunk 124 optimal weight: 0.6980 chunk 58 optimal weight: 0.0070 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.090455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068457 restraints weight = 72445.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070362 restraints weight = 36430.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.071567 restraints weight = 23683.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072227 restraints weight = 18246.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072724 restraints weight = 15799.584| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5966 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= 0.149 Angle : 0.818 18.700 27788 Z= 0.401 Chirality : 0.048 0.347 3375 Planarity : 0.005 0.059 2884 Dihedral : 21.924 172.454 4744 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.87 % Favored : 92.88 % Rotamer: Outliers : 3.97 % Allowed : 28.73 % 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 aren not related in a simple way. whole: -1.14 (0.19), residues: 1966 helix: 1.07 (0.20), residues: 722 sheet: -1.58 (0.28), residues: 325 loop : -1.98 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 52 TYR 0.027 0.002 TYR A 417 PHE 0.031 0.002 PHE d 63 TRP 0.031 0.001 TRP C 933 HIS 0.011 0.001 HIS j 52 Details of bonding type rmsd covalent geometry : bond 0.00329 (19870) covalent geometry : angle 0.81837 (27788) hydrogen bonds : bond 0.05631 ( 616) hydrogen bonds : angle 4.31778 ( 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 388 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 323 time to evaluate : 0.689 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 134 MET cc_start: 0.8089 (mpp) cc_final: 0.7797 (ptp) REVERT: A 175 LEU cc_start: 0.9385 (tt) cc_final: 0.9128 (tt) REVERT: A 283 SER cc_start: 0.8482 (p) cc_final: 0.8217 (m) REVERT: A 303 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: A 364 TYR cc_start: 0.4538 (OUTLIER) cc_final: 0.3161 (m-80) REVERT: A 529 TYR cc_start: 0.9180 (t80) cc_final: 0.8946 (t80) REVERT: A 649 LEU cc_start: 0.9360 (tp) cc_final: 0.9080 (tp) REVERT: A 674 MET cc_start: 0.8526 (tpt) cc_final: 0.8079 (tpt) REVERT: A 701 CYS cc_start: 0.7771 (t) cc_final: 0.7412 (t) REVERT: C 150 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7584 (mmt) REVERT: C 210 ILE cc_start: 0.9436 (mm) cc_final: 0.9138 (mm) REVERT: C 387 TYR cc_start: 0.8002 (m-80) cc_final: 0.7684 (m-80) REVERT: C 473 LEU cc_start: 0.9383 (mt) cc_final: 0.9098 (mt) REVERT: C 574 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 653 ASP cc_start: 0.7794 (t0) cc_final: 0.7480 (t0) REVERT: C 674 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 842 MET cc_start: 0.7650 (tpp) cc_final: 0.7283 (tpp) REVERT: C 869 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.7912 (m90) REVERT: b 5 GLN cc_start: 0.7918 (pm20) cc_final: 0.7501 (tm-30) REVERT: b 12 LEU cc_start: 0.9082 (tp) cc_final: 0.8838 (pp) REVERT: b 18 TYR cc_start: 0.8105 (m-80) cc_final: 0.7862 (m-80) REVERT: b 28 ARG cc_start: 0.8461 (mmp80) cc_final: 0.7931 (mmp80) REVERT: b 35 MET cc_start: 0.8516 (mmm) cc_final: 0.8168 (mpp) REVERT: b 90 GLU cc_start: 0.8033 (tp30) cc_final: 0.7730 (tp30) REVERT: h 93 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7787 (tpp80) REVERT: j 92 SER cc_start: 0.9229 (m) cc_final: 0.8837 (p) REVERT: j 93 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.6796 (mttt) REVERT: j 95 PHE cc_start: 0.8019 (t80) cc_final: 0.7725 (t80) outliers start: 65 outliers final: 47 residues processed: 362 average time/residue: 0.1316 time to fit residues: 76.6030 Evaluate side-chains 361 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 364 TYR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 259 ASN 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 432 GLN 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 493 LEU Chi-restraints excluded: chain C residue 574 SER 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 773 VAL Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 23 GLN 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 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 57 THR 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 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 93 LYS 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: 0.2980 chunk 194 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.090411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068214 restraints weight = 71633.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070140 restraints weight = 35462.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071411 restraints weight = 22892.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072180 restraints weight = 17426.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072563 restraints weight = 14887.498| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 19870 Z= 0.222 Angle : 0.946 59.179 27788 Z= 0.504 Chirality : 0.051 1.059 3375 Planarity : 0.005 0.059 2884 Dihedral : 21.923 172.436 4742 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.92 % Favored : 92.78 % Rotamer: Outliers : 3.61 % Allowed : 29.71 % Favored : 66.69 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: -1.16 (0.19), residues: 1966 helix: 1.04 (0.20), residues: 723 sheet: -1.57 (0.29), residues: 320 loop : -1.99 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG h 93 TYR 0.023 0.002 TYR A 417 PHE 0.029 0.002 PHE j 24 TRP 0.028 0.001 TRP C 933 HIS 0.008 0.001 HIS j 52 Details of bonding type rmsd covalent geometry : bond 0.00482 (19870) covalent geometry : angle 0.94604 (27788) hydrogen bonds : bond 0.05632 ( 616) hydrogen bonds : angle 4.32553 ( 1661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.65 seconds wall clock time: 64 minutes 44.36 seconds (3884.36 seconds total)