Starting phenix.real_space_refine on Sat Jul 4 01:33:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avg_43901/07_2026/9avg_43901.map" } resolution = 3.6 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= 0.002 sd= 0.040 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 P 3 5.49 5 S 93 5.16 5 Cl 2 4.86 5 C 11311 2.51 5 N 2883 2.21 5 O 3200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17498 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6280 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 6294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6294 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1738 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2450 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 61 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'NAG': 2, 'TCR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Time building chain proxies: 3.64, per 1000 atoms: 0.21 Number of scatterers: 17498 At special positions: 0 Unit cell: (117.15, 97.35, 237.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 93 16.00 P 3 15.00 O 3200 8.00 N 2883 7.00 C 11311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 437 " - pdb=" SG CYS Q 449 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 287 " " NAG R1002 " - " ASN R 468 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 748.5 milliseconds 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 24 sheets defined 45.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 83 Processing helix chain 'Q' and resid 103 through 113 Processing helix chain 'Q' and resid 115 through 123 Processing helix chain 'Q' and resid 146 through 158 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.609A pdb=" N LEU Q 174 " --> pdb=" O SER Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.551A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 438 through 442 removed outlier: 3.866A pdb=" N GLY Q 442 " --> pdb=" O PRO Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 456 through 466 Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 removed outlier: 3.755A pdb=" N THR Q 646 " --> pdb=" O ILE Q 642 " (cutoff:3.500A) Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.729A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 669 Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.976A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 702 through 708 Processing helix chain 'Q' and resid 723 through 746 removed outlier: 4.092A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 793 removed outlier: 3.721A pdb=" N LYS Q 793 " --> pdb=" O PHE Q 789 " (cutoff:3.500A) Processing helix chain 'Q' and resid 802 through 820 Processing helix chain 'Q' and resid 820 through 827 removed outlier: 3.690A pdb=" N ALA Q 824 " --> pdb=" O SER Q 820 " (cutoff:3.500A) Processing helix chain 'Q' and resid 831 through 862 removed outlier: 4.093A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 3.663A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 115 Processing helix chain 'R' and resid 115 through 122 Processing helix chain 'R' and resid 146 through 158 removed outlier: 3.641A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.503A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 272 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 4.413A pdb=" N SER R 301 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 451 through 455 removed outlier: 3.843A pdb=" N VAL R 455 " --> pdb=" O ILE R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 465 Processing helix chain 'R' and resid 525 through 528 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 645 Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.630A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 669 Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.752A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix Processing helix chain 'R' and resid 719 through 746 Processing helix chain 'R' and resid 770 through 794 removed outlier: 3.632A pdb=" N THR R 780 " --> pdb=" O LEU R 776 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA R 785 " --> pdb=" O CYS R 781 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 821 Processing helix chain 'R' and resid 821 through 827 removed outlier: 3.771A pdb=" N SER R 827 " --> pdb=" O PRO R 823 " (cutoff:3.500A) Processing helix chain 'R' and resid 830 through 861 removed outlier: 3.970A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.739A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.163A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.715A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.504A pdb=" N ALA A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.365A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.154A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.653A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.054A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN Q 164 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 41 through 44 removed outlier: 6.247A pdb=" N HIS Q 41 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR Q 63 " --> pdb=" O HIS Q 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 236 through 243 removed outlier: 7.954A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA6, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA7, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA8, first strand: chain 'Q' and resid 602 through 604 Processing sheet with id=AA9, first strand: chain 'R' and resid 25 through 28 removed outlier: 6.212A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN R 164 " --> pdb=" O LEU R 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 236 through 243 removed outlier: 6.556A pdb=" N VAL R 209 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE R 239 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE R 267 " --> pdb=" O LEU R 294 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TRP R 293 " --> pdb=" O ILE R 318 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE R 320 " --> pdb=" O TRP R 293 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA R 295 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU R 322 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.525A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604 removed outlier: 5.970A pdb=" N GLU R 602 " --> pdb=" O ILE R 761 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE R 763 " --> pdb=" O GLU R 602 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU R 604 " --> pdb=" O ILE R 763 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N CYS R 765 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.884A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.847A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.744A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.751A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.934A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.929A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.402A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.789A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4666 1.33 - 1.45: 3780 1.45 - 1.58: 9345 1.58 - 1.70: 2 1.70 - 1.82: 114 Bond restraints: 17907 Sorted by residual: bond pdb=" CAI Y01 Q1010 " pdb=" CAK Y01 Q1010 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CB TCR R1003 " pdb=" CG TCR R1003 " ideal model delta sigma weight residual 1.494 1.426 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3 PO4 R1004 " pdb=" P PO4 R1004 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O2 PO4 R1004 " pdb=" P PO4 R1004 " ideal model delta sigma weight residual 1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 17902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23964 2.35 - 4.69: 331 4.69 - 7.04: 25 7.04 - 9.39: 5 9.39 - 11.74: 3 Bond angle restraints: 24328 Sorted by residual: angle pdb=" C ALA A 7 " pdb=" CA ALA A 7 " pdb=" CB ALA A 7 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 angle pdb=" C LEU R 743 " pdb=" N TYR R 744 " pdb=" CA TYR R 744 " ideal model delta sigma weight residual 122.26 115.93 6.33 1.59e+00 3.96e-01 1.59e+01 angle pdb=" OAG Y01 Q1010 " pdb=" CAY Y01 Q1010 " pdb=" OAW Y01 Q1010 " ideal model delta sigma weight residual 123.38 111.64 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAM Y01 Q1010 " pdb=" CAY Y01 Q1010 " pdb=" OAW Y01 Q1010 " ideal model delta sigma weight residual 111.19 122.63 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N ILE A 193 " pdb=" CA ILE A 193 " pdb=" CB ILE A 193 " ideal model delta sigma weight residual 110.55 114.66 -4.11 1.17e+00 7.31e-01 1.23e+01 ... (remaining 24323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 9874 18.06 - 36.12: 742 36.12 - 54.18: 112 54.18 - 72.24: 30 72.24 - 90.29: 8 Dihedral angle restraints: 10766 sinusoidal: 4338 harmonic: 6428 Sorted by residual: dihedral pdb=" CA PHE A 142 " pdb=" C PHE A 142 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE Q 852 " pdb=" C ILE Q 852 " pdb=" N PHE Q 853 " pdb=" CA PHE Q 853 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 10763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2138 0.048 - 0.097: 525 0.097 - 0.145: 117 0.145 - 0.194: 6 0.194 - 0.242: 4 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C02 A1AF7 R1009 " pdb=" C01 A1AF7 R1009 " pdb=" C03 A1AF7 R1009 " pdb=" O01 A1AF7 R1009 " both_signs ideal model delta sigma weight residual False 2.54 2.78 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1 NAG Q1002 " pdb=" ND2 ASN Q 287 " pdb=" C2 NAG Q1002 " pdb=" O5 NAG Q1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE B 81 " pdb=" CA ILE B 81 " pdb=" CG1 ILE B 81 " pdb=" CG2 ILE B 81 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2787 not shown) Planarity restraints: 3065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 54 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO R 55 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 55 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 55 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS Q 568 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO Q 569 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO Q 569 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Q 569 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 850 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ALA Q 850 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA Q 850 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS Q 851 " -0.014 2.00e-02 2.50e+03 ... (remaining 3062 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 280 2.67 - 3.23: 17178 3.23 - 3.78: 28491 3.78 - 4.34: 39608 4.34 - 4.90: 63001 Nonbonded interactions: 148558 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.112 3.040 nonbonded pdb=" O MET A 18 " pdb=" NE2 GLN A 22 " model vdw 2.207 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.218 3.120 nonbonded pdb=" OD2 ASP R 238 " pdb=" OG SER R 262 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR R 470 " pdb=" OE1 GLN R 476 " model vdw 2.226 3.040 ... (remaining 148553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 22 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 120 or (resid 121 and (name N or n \ ame CA or name C or name O or name CB )) or resid 122 or resid 135 through 230 o \ r (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 32 through 360 or (resid 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 404 or (resid 405 and (name N or name CA or name C or \ name O or name CB )) or resid 406 through 518 or (resid 519 and (name N or name \ CA or name C or name O or name CB )) or resid 520 through 864 or resid 1002 thr \ ough 1009)) selection = (chain 'R' and (resid 22 through 46 or (resid 47 through 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 55 or (resid 56 and (na \ me N or name CA or name C or name O or name CB )) or resid 57 through 247 or (re \ sid 248 through 250 and (name N or name CA or name C or name O or name CB )) or \ resid 251 through 453 or (resid 454 and (name N or name CA or name C or name O o \ r name CB )) or resid 455 through 499 or (resid 500 and (name N or name CA or na \ me C or name O or name CB )) or resid 501 through 525 or (resid 526 and (name N \ or name CA or name C or name O or name CB )) or resid 527 through 609 or (resid \ 610 and (name N or name CA or name C or name O or name CB )) or resid 611 throug \ h 637 or (resid 638 and (name N or name CA or name C or name O or name CB )) or \ resid 639 through 708 or resid 722 through 1008)) } 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: 13.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.080 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.005 0.086 17936 Z= 0.234 Angle : 0.700 11.736 24399 Z= 0.383 Chirality : 0.044 0.242 2790 Planarity : 0.005 0.082 3056 Dihedral : 12.938 90.294 6554 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2182 helix: 0.25 (0.16), residues: 911 sheet: -1.52 (0.26), residues: 371 loop : -0.80 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 25 TYR 0.014 0.002 TYR B 289 PHE 0.033 0.002 PHE Q 634 TRP 0.023 0.002 TRP R 352 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (17907) covalent geometry : angle 0.69211 / 0.38 (24328) SS BOND : bond 0.00137 / 0.10 ( 16) SS BOND : angle 0.78833 / 0.57 ( 32) hydrogen bonds : bond 0.13694 / 9.24 ( 837) hydrogen bonds : angle 6.14320 / 4.42 ( 2406) link_BETA1-4 : bond 0.00486 / 0.27 ( 4) link_BETA1-4 : angle 1.17892 / 0.76 ( 12) link_NAG-ASN : bond 0.00404 / 0.29 ( 9) link_NAG-ASN : angle 3.05728 / 1.88 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 92 THR cc_start: 0.6822 (t) cc_final: 0.6593 (t) REVERT: R 248 ASP cc_start: 0.6710 (m-30) cc_final: 0.6418 (m-30) REVERT: R 309 GLN cc_start: 0.8048 (pm20) cc_final: 0.7666 (pm20) REVERT: A 38 LEU cc_start: 0.8231 (tp) cc_final: 0.8013 (tp) REVERT: A 122 LEU cc_start: 0.7931 (tp) cc_final: 0.7643 (tp) REVERT: A 235 ILE cc_start: 0.8711 (mm) cc_final: 0.8403 (mp) REVERT: B 36 ASN cc_start: 0.5165 (m-40) cc_final: 0.4784 (p0) REVERT: B 81 ILE cc_start: 0.8370 (tp) cc_final: 0.8158 (tp) REVERT: B 333 ASP cc_start: 0.7677 (p0) cc_final: 0.6411 (t0) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1294 time to fit residues: 74.7550 Evaluate side-chains 348 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098983 restraints weight = 28303.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098926 restraints weight = 24092.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100169 restraints weight = 22342.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100561 restraints weight = 17350.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100693 restraints weight = 15339.821| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17936 Z= 0.169 Angle : 0.560 7.768 24399 Z= 0.298 Chirality : 0.043 0.171 2790 Planarity : 0.005 0.065 3056 Dihedral : 7.575 64.927 2791 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.94 % Allowed : 6.83 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2182 helix: 0.67 (0.16), residues: 918 sheet: -1.48 (0.26), residues: 373 loop : -0.72 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 62 TYR 0.013 0.002 TYR R 421 PHE 0.022 0.002 PHE R 788 TRP 0.017 0.002 TRP B 297 HIS 0.009 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (17907) covalent geometry : angle 0.55456 / 0.30 (24328) SS BOND : bond 0.00127 / 0.09 ( 16) SS BOND : angle 0.80744 / 0.53 ( 32) hydrogen bonds : bond 0.05043 / 3.33 ( 837) hydrogen bonds : angle 4.99384 / 3.66 ( 2406) link_BETA1-4 : bond 0.00451 / 0.26 ( 4) link_BETA1-4 : angle 1.08544 / 0.70 ( 12) link_NAG-ASN : bond 0.00507 / 0.33 ( 9) link_NAG-ASN : angle 2.13548 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 373 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 261 ASN cc_start: 0.6405 (m110) cc_final: 0.6037 (t0) REVERT: Q 860 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7711 (mt) REVERT: R 248 ASP cc_start: 0.6540 (m-30) cc_final: 0.6131 (m-30) REVERT: R 282 GLU cc_start: 0.6637 (tp30) cc_final: 0.6423 (tp30) REVERT: R 309 GLN cc_start: 0.8061 (pm20) cc_final: 0.7494 (pm20) REVERT: A 122 LEU cc_start: 0.7649 (tp) cc_final: 0.7360 (tp) REVERT: A 234 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 235 ILE cc_start: 0.8712 (mm) cc_final: 0.8395 (mp) REVERT: B 71 VAL cc_start: 0.8534 (m) cc_final: 0.8307 (t) REVERT: B 198 LEU cc_start: 0.8898 (mm) cc_final: 0.8583 (mp) REVERT: B 263 THR cc_start: 0.6944 (m) cc_final: 0.6525 (p) outliers start: 17 outliers final: 14 residues processed: 378 average time/residue: 0.1283 time to fit residues: 73.2756 Evaluate side-chains 361 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 345 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098054 restraints weight = 28637.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098416 restraints weight = 24662.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099097 restraints weight = 24794.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099598 restraints weight = 19151.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099752 restraints weight = 16294.709| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17936 Z= 0.171 Angle : 0.545 10.871 24399 Z= 0.287 Chirality : 0.043 0.161 2790 Planarity : 0.004 0.048 3056 Dihedral : 7.263 68.913 2791 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.89 % Allowed : 9.32 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2182 helix: 0.81 (0.16), residues: 920 sheet: -1.40 (0.26), residues: 371 loop : -0.66 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 185 TYR 0.019 0.002 TYR R 744 PHE 0.022 0.002 PHE B 241 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS Q 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (17907) covalent geometry : angle 0.53964 / 0.29 (24328) SS BOND : bond 0.00134 / 0.10 ( 16) SS BOND : angle 1.09084 / 0.68 ( 32) hydrogen bonds : bond 0.04818 / 3.16 ( 837) hydrogen bonds : angle 4.80109 / 3.53 ( 2406) link_BETA1-4 : bond 0.00289 / 0.16 ( 4) link_BETA1-4 : angle 1.07678 / 0.69 ( 12) link_NAG-ASN : bond 0.00437 / 0.31 ( 9) link_NAG-ASN : angle 2.05212 / 1.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7093 (OUTLIER) cc_final: 0.6729 (t) REVERT: R 248 ASP cc_start: 0.6507 (m-30) cc_final: 0.6157 (m-30) REVERT: R 309 GLN cc_start: 0.8063 (pm20) cc_final: 0.7714 (pm20) REVERT: R 422 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 122 LEU cc_start: 0.7663 (tp) cc_final: 0.7358 (tp) REVERT: A 234 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 36 ASN cc_start: 0.5181 (m-40) cc_final: 0.4870 (p0) REVERT: B 71 VAL cc_start: 0.8473 (m) cc_final: 0.7997 (t) REVERT: B 81 ILE cc_start: 0.8542 (tp) cc_final: 0.8128 (tp) REVERT: B 198 LEU cc_start: 0.8887 (mm) cc_final: 0.8586 (mp) REVERT: B 263 THR cc_start: 0.6949 (m) cc_final: 0.6474 (p) outliers start: 34 outliers final: 21 residues processed: 373 average time/residue: 0.1268 time to fit residues: 71.8395 Evaluate side-chains 368 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 344 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 612 PHE Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 141 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 109 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098252 restraints weight = 28587.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098157 restraints weight = 23118.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099075 restraints weight = 22557.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099545 restraints weight = 17627.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099906 restraints weight = 15246.966| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17936 Z= 0.174 Angle : 0.534 7.468 24399 Z= 0.281 Chirality : 0.043 0.188 2790 Planarity : 0.004 0.048 3056 Dihedral : 7.036 71.266 2791 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.50 % Allowed : 10.93 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2182 helix: 0.84 (0.16), residues: 923 sheet: -1.36 (0.26), residues: 370 loop : -0.67 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 314 TYR 0.020 0.002 TYR R 744 PHE 0.021 0.002 PHE A 100 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (17907) covalent geometry : angle 0.52849 / 0.28 (24328) SS BOND : bond 0.00181 / 0.13 ( 16) SS BOND : angle 1.06143 / 0.68 ( 32) hydrogen bonds : bond 0.04710 / 3.08 ( 837) hydrogen bonds : angle 4.71198 / 3.47 ( 2406) link_BETA1-4 : bond 0.00245 / 0.13 ( 4) link_BETA1-4 : angle 1.06361 / 0.69 ( 12) link_NAG-ASN : bond 0.00453 / 0.32 ( 9) link_NAG-ASN : angle 2.13550 / 1.22 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 594 ASN cc_start: 0.6769 (m110) cc_final: 0.6185 (m-40) REVERT: Q 702 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6712 (t) REVERT: R 248 ASP cc_start: 0.6490 (m-30) cc_final: 0.6135 (m-30) REVERT: R 277 GLU cc_start: 0.7888 (tt0) cc_final: 0.7448 (tt0) REVERT: R 282 GLU cc_start: 0.6657 (tp30) cc_final: 0.6429 (tp30) REVERT: R 309 GLN cc_start: 0.8059 (pm20) cc_final: 0.7705 (pm20) REVERT: R 422 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7609 (mp) REVERT: A 106 ILE cc_start: 0.8288 (mm) cc_final: 0.7972 (mm) REVERT: A 122 LEU cc_start: 0.7734 (tp) cc_final: 0.7407 (tp) REVERT: A 234 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 235 ILE cc_start: 0.8680 (mm) cc_final: 0.8446 (mp) REVERT: B 36 ASN cc_start: 0.5163 (m-40) cc_final: 0.4894 (p0) REVERT: B 198 LEU cc_start: 0.8895 (mm) cc_final: 0.8612 (mp) REVERT: B 263 THR cc_start: 0.6989 (m) cc_final: 0.6468 (p) REVERT: B 314 ARG cc_start: 0.8366 (mtm110) cc_final: 0.7970 (mtp-110) outliers start: 45 outliers final: 29 residues processed: 378 average time/residue: 0.1306 time to fit residues: 74.4694 Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 76 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098670 restraints weight = 28309.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098737 restraints weight = 24126.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099841 restraints weight = 23498.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100192 restraints weight = 17935.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100457 restraints weight = 15722.904| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17936 Z= 0.156 Angle : 0.521 6.682 24399 Z= 0.274 Chirality : 0.043 0.224 2790 Planarity : 0.004 0.047 3056 Dihedral : 6.772 71.824 2791 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.22 % Allowed : 12.32 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2182 helix: 0.95 (0.16), residues: 922 sheet: -1.26 (0.26), residues: 358 loop : -0.63 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 535 TYR 0.021 0.001 TYR R 744 PHE 0.021 0.002 PHE A 100 TRP 0.013 0.001 TRP Q 299 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (17907) covalent geometry : angle 0.51481 / 0.27 (24328) SS BOND : bond 0.00142 / 0.10 ( 16) SS BOND : angle 0.86269 / 0.59 ( 32) hydrogen bonds : bond 0.04556 / 2.98 ( 837) hydrogen bonds : angle 4.61575 / 3.39 ( 2406) link_BETA1-4 : bond 0.00272 / 0.15 ( 4) link_BETA1-4 : angle 1.04798 / 0.66 ( 12) link_NAG-ASN : bond 0.00367 / 0.26 ( 9) link_NAG-ASN : angle 2.28984 / 1.34 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 361 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7081 (OUTLIER) cc_final: 0.6686 (t) REVERT: R 248 ASP cc_start: 0.6517 (m-30) cc_final: 0.6192 (m-30) REVERT: R 277 GLU cc_start: 0.7877 (tt0) cc_final: 0.7422 (tt0) REVERT: R 309 GLN cc_start: 0.8097 (pm20) cc_final: 0.7725 (pm20) REVERT: R 422 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 106 ILE cc_start: 0.8336 (mm) cc_final: 0.7927 (mm) REVERT: A 122 LEU cc_start: 0.7657 (tp) cc_final: 0.7340 (tp) REVERT: A 234 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 235 ILE cc_start: 0.8644 (mm) cc_final: 0.8350 (mp) REVERT: B 36 ASN cc_start: 0.5187 (m-40) cc_final: 0.4866 (p0) REVERT: B 81 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 198 LEU cc_start: 0.8872 (mm) cc_final: 0.8613 (mp) REVERT: B 314 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7927 (mtp-110) outliers start: 40 outliers final: 26 residues processed: 381 average time/residue: 0.1341 time to fit residues: 77.0986 Evaluate side-chains 366 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 33 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 25 optimal weight: 0.0870 chunk 192 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 155 optimal weight: 0.9980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098636 restraints weight = 28315.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098727 restraints weight = 22309.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099687 restraints weight = 21861.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100199 restraints weight = 16580.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100369 restraints weight = 14333.566| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17936 Z= 0.135 Angle : 0.508 6.944 24399 Z= 0.267 Chirality : 0.042 0.144 2790 Planarity : 0.004 0.048 3056 Dihedral : 6.589 70.446 2791 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.33 % Allowed : 13.54 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2182 helix: 1.06 (0.16), residues: 927 sheet: -1.24 (0.26), residues: 361 loop : -0.65 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.021 0.001 TYR R 744 PHE 0.029 0.001 PHE A 100 TRP 0.012 0.001 TRP Q 299 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (17907) covalent geometry : angle 0.50019 / 0.26 (24328) SS BOND : bond 0.00198 / 0.14 ( 16) SS BOND : angle 1.24826 / 0.77 ( 32) hydrogen bonds : bond 0.04407 / 2.89 ( 837) hydrogen bonds : angle 4.51580 / 3.31 ( 2406) link_BETA1-4 : bond 0.00262 / 0.15 ( 4) link_BETA1-4 : angle 1.01423 / 0.59 ( 12) link_NAG-ASN : bond 0.00312 / 0.23 ( 9) link_NAG-ASN : angle 2.31524 / 1.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 248 ASP cc_start: 0.6513 (m-30) cc_final: 0.6162 (m-30) REVERT: R 277 GLU cc_start: 0.7872 (tt0) cc_final: 0.7408 (tt0) REVERT: R 309 GLN cc_start: 0.8114 (pm20) cc_final: 0.7725 (pm20) REVERT: R 422 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7609 (mp) REVERT: R 526 GLU cc_start: 0.6704 (pp20) cc_final: 0.6425 (pp20) REVERT: A 106 ILE cc_start: 0.8334 (mm) cc_final: 0.7968 (mm) REVERT: A 122 LEU cc_start: 0.7642 (tp) cc_final: 0.7343 (tp) REVERT: B 36 ASN cc_start: 0.5180 (m-40) cc_final: 0.4900 (p0) REVERT: B 198 LEU cc_start: 0.8858 (mm) cc_final: 0.8610 (mp) REVERT: B 314 ARG cc_start: 0.8300 (mtm110) cc_final: 0.7931 (mtp-110) outliers start: 42 outliers final: 29 residues processed: 379 average time/residue: 0.1333 time to fit residues: 77.0930 Evaluate side-chains 368 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097465 restraints weight = 28543.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097640 restraints weight = 24058.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098348 restraints weight = 25367.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098871 restraints weight = 19331.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099199 restraints weight = 16621.420| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17936 Z= 0.193 Angle : 0.549 7.466 24399 Z= 0.289 Chirality : 0.043 0.162 2790 Planarity : 0.004 0.062 3056 Dihedral : 6.656 70.937 2791 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.50 % Allowed : 13.87 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2182 helix: 0.96 (0.16), residues: 925 sheet: -1.26 (0.26), residues: 362 loop : -0.67 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.021 0.002 TYR R 744 PHE 0.021 0.002 PHE R 444 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS Q 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (17907) covalent geometry : angle 0.54001 / 0.29 (24328) SS BOND : bond 0.00164 / 0.12 ( 16) SS BOND : angle 1.34684 / 0.81 ( 32) hydrogen bonds : bond 0.04674 / 3.07 ( 837) hydrogen bonds : angle 4.63213 / 3.39 ( 2406) link_BETA1-4 : bond 0.00259 / 0.14 ( 4) link_BETA1-4 : angle 1.10110 / 0.72 ( 12) link_NAG-ASN : bond 0.00379 / 0.30 ( 9) link_NAG-ASN : angle 2.61231 / 1.50 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 351 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 248 ASP cc_start: 0.6539 (m-30) cc_final: 0.6195 (m-30) REVERT: R 277 GLU cc_start: 0.7888 (tt0) cc_final: 0.7425 (tt0) REVERT: R 282 GLU cc_start: 0.6725 (tp30) cc_final: 0.6348 (tp30) REVERT: R 309 GLN cc_start: 0.8082 (pm20) cc_final: 0.7698 (pm20) REVERT: R 422 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7668 (mp) REVERT: R 526 GLU cc_start: 0.6719 (pp20) cc_final: 0.6430 (pp20) REVERT: R 795 ARG cc_start: 0.7598 (ptt-90) cc_final: 0.7335 (ptt-90) REVERT: A 13 VAL cc_start: 0.7712 (m) cc_final: 0.7305 (t) REVERT: A 106 ILE cc_start: 0.8345 (mm) cc_final: 0.8015 (mm) REVERT: A 122 LEU cc_start: 0.7656 (tp) cc_final: 0.7356 (tp) REVERT: B 198 LEU cc_start: 0.8876 (mm) cc_final: 0.8616 (mp) REVERT: B 314 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7919 (mtp-110) outliers start: 45 outliers final: 34 residues processed: 375 average time/residue: 0.1414 time to fit residues: 80.0294 Evaluate side-chains 377 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 84 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097547 restraints weight = 28492.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097272 restraints weight = 22867.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097691 restraints weight = 22756.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098178 restraints weight = 19768.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098358 restraints weight = 16560.910| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17936 Z= 0.225 Angle : 0.581 8.597 24399 Z= 0.307 Chirality : 0.044 0.143 2790 Planarity : 0.004 0.056 3056 Dihedral : 6.771 72.757 2791 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.61 % Allowed : 14.37 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2182 helix: 0.85 (0.16), residues: 923 sheet: -1.26 (0.26), residues: 352 loop : -0.69 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 135 TYR 0.021 0.002 TYR R 744 PHE 0.025 0.002 PHE R 444 TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS Q 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (17907) covalent geometry : angle 0.57223 / 0.30 (24328) SS BOND : bond 0.00232 / 0.17 ( 16) SS BOND : angle 1.74009 / 1.08 ( 32) hydrogen bonds : bond 0.04851 / 3.19 ( 837) hydrogen bonds : angle 4.71891 / 3.46 ( 2406) link_BETA1-4 : bond 0.00250 / 0.14 ( 4) link_BETA1-4 : angle 1.13191 / 0.75 ( 12) link_NAG-ASN : bond 0.00456 / 0.35 ( 9) link_NAG-ASN : angle 2.42847 / 1.37 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 358 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: Q 561 CYS cc_start: 0.5008 (m) cc_final: 0.4781 (m) REVERT: R 248 ASP cc_start: 0.6527 (m-30) cc_final: 0.6179 (m-30) REVERT: R 309 GLN cc_start: 0.8076 (pm20) cc_final: 0.7690 (pm20) REVERT: R 422 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7675 (mp) REVERT: R 526 GLU cc_start: 0.6733 (pp20) cc_final: 0.6441 (pp20) REVERT: A 13 VAL cc_start: 0.7764 (m) cc_final: 0.7379 (t) REVERT: A 106 ILE cc_start: 0.8360 (mm) cc_final: 0.8022 (mm) REVERT: A 122 LEU cc_start: 0.7739 (tp) cc_final: 0.7429 (tp) REVERT: B 36 ASN cc_start: 0.5257 (m-40) cc_final: 0.4953 (p0) REVERT: B 198 LEU cc_start: 0.8909 (mm) cc_final: 0.8645 (mp) REVERT: B 285 LEU cc_start: 0.8916 (tp) cc_final: 0.8510 (tt) REVERT: B 314 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7914 (mtp-110) outliers start: 47 outliers final: 36 residues processed: 383 average time/residue: 0.1398 time to fit residues: 80.9854 Evaluate side-chains 381 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 152 optimal weight: 0.3980 chunk 154 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 189 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 156 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098180 restraints weight = 28566.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098314 restraints weight = 23052.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098947 restraints weight = 23107.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099493 restraints weight = 17901.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099618 restraints weight = 15957.663| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17936 Z= 0.144 Angle : 0.569 15.035 24399 Z= 0.294 Chirality : 0.042 0.203 2790 Planarity : 0.004 0.057 3056 Dihedral : 6.635 71.908 2791 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 15.70 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2182 helix: 0.92 (0.16), residues: 932 sheet: -1.22 (0.26), residues: 360 loop : -0.68 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.020 0.001 TYR R 744 PHE 0.023 0.002 PHE A 100 TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS R 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (17907) covalent geometry : angle 0.54817 / 0.29 (24328) SS BOND : bond 0.00156 / 0.11 ( 16) SS BOND : angle 1.25595 / 0.80 ( 32) hydrogen bonds : bond 0.04483 / 2.95 ( 837) hydrogen bonds : angle 4.62227 / 3.39 ( 2406) link_BETA1-4 : bond 0.00308 / 0.17 ( 4) link_BETA1-4 : angle 1.05514 / 0.66 ( 12) link_NAG-ASN : bond 0.00308 / 0.23 ( 9) link_NAG-ASN : angle 4.40304 / 3.34 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: Q 436 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7944 (p) REVERT: Q 561 CYS cc_start: 0.5004 (m) cc_final: 0.4777 (m) REVERT: R 248 ASP cc_start: 0.6540 (m-30) cc_final: 0.6176 (m-30) REVERT: R 277 GLU cc_start: 0.7883 (tt0) cc_final: 0.7408 (tt0) REVERT: R 309 GLN cc_start: 0.8120 (pm20) cc_final: 0.7728 (pm20) REVERT: R 422 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7686 (mp) REVERT: R 526 GLU cc_start: 0.6709 (pp20) cc_final: 0.6420 (pp20) REVERT: R 592 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7675 (p0) REVERT: R 679 LEU cc_start: 0.6706 (tp) cc_final: 0.6368 (mt) REVERT: A 106 ILE cc_start: 0.8373 (mm) cc_final: 0.8028 (mm) REVERT: A 122 LEU cc_start: 0.7679 (tp) cc_final: 0.7384 (tp) REVERT: B 36 ASN cc_start: 0.5130 (m-40) cc_final: 0.4898 (p0) REVERT: B 198 LEU cc_start: 0.8886 (mm) cc_final: 0.8599 (mp) REVERT: B 285 LEU cc_start: 0.8913 (tp) cc_final: 0.8501 (tt) REVERT: B 311 HIS cc_start: 0.6359 (m-70) cc_final: 0.6052 (t-90) REVERT: B 314 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7943 (mtp-110) outliers start: 38 outliers final: 29 residues processed: 365 average time/residue: 0.1382 time to fit residues: 76.4901 Evaluate side-chains 367 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 334 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 169 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.0050 chunk 134 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098584 restraints weight = 28091.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098516 restraints weight = 22051.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099711 restraints weight = 20963.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099974 restraints weight = 16500.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100113 restraints weight = 14698.263| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17936 Z= 0.151 Angle : 0.563 11.892 24399 Z= 0.294 Chirality : 0.042 0.193 2790 Planarity : 0.004 0.058 3056 Dihedral : 6.572 70.963 2791 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.11 % Allowed : 15.82 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2182 helix: 0.94 (0.16), residues: 931 sheet: -1.16 (0.26), residues: 370 loop : -0.69 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.020 0.002 TYR R 744 PHE 0.022 0.002 PHE A 100 TRP 0.018 0.002 TRP B 169 HIS 0.003 0.001 HIS Q 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (17907) covalent geometry : angle 0.54841 / 0.29 (24328) SS BOND : bond 0.00121 / 0.09 ( 16) SS BOND : angle 1.11820 / 0.76 ( 32) hydrogen bonds : bond 0.04468 / 2.95 ( 837) hydrogen bonds : angle 4.61589 / 3.39 ( 2406) link_BETA1-4 : bond 0.00279 / 0.16 ( 4) link_BETA1-4 : angle 1.05400 / 0.66 ( 12) link_NAG-ASN : bond 0.00236 / 0.17 ( 9) link_NAG-ASN : angle 3.62079 / 2.71 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: Q 561 CYS cc_start: 0.5012 (m) cc_final: 0.4778 (m) REVERT: R 248 ASP cc_start: 0.6550 (m-30) cc_final: 0.6237 (m-30) REVERT: R 277 GLU cc_start: 0.7887 (tt0) cc_final: 0.7430 (tt0) REVERT: R 282 GLU cc_start: 0.6769 (tp30) cc_final: 0.6370 (tp30) REVERT: R 309 GLN cc_start: 0.8096 (pm20) cc_final: 0.7695 (pm20) REVERT: R 422 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7675 (mp) REVERT: R 526 GLU cc_start: 0.6728 (pp20) cc_final: 0.6420 (pp20) REVERT: R 679 LEU cc_start: 0.6672 (tp) cc_final: 0.6291 (mt) REVERT: R 795 ARG cc_start: 0.7499 (ptt-90) cc_final: 0.7043 (ptt90) REVERT: A 106 ILE cc_start: 0.8396 (mm) cc_final: 0.8083 (mm) REVERT: A 122 LEU cc_start: 0.7720 (tp) cc_final: 0.7414 (tp) REVERT: B 198 LEU cc_start: 0.8894 (mm) cc_final: 0.8609 (mp) REVERT: B 285 LEU cc_start: 0.8894 (tp) cc_final: 0.8486 (tt) REVERT: B 314 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7868 (mtp-110) outliers start: 38 outliers final: 29 residues processed: 355 average time/residue: 0.1242 time to fit residues: 66.7689 Evaluate side-chains 366 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 335 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 197 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 139 optimal weight: 0.0670 chunk 105 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098770 restraints weight = 28584.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098873 restraints weight = 22733.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099986 restraints weight = 21183.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100504 restraints weight = 17025.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101654 restraints weight = 16279.908| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17936 Z= 0.145 Angle : 0.547 10.693 24399 Z= 0.288 Chirality : 0.042 0.190 2790 Planarity : 0.004 0.057 3056 Dihedral : 6.490 69.982 2791 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.11 % Allowed : 15.93 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2182 helix: 0.97 (0.16), residues: 932 sheet: -1.09 (0.26), residues: 352 loop : -0.69 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.019 0.001 TYR R 744 PHE 0.030 0.002 PHE A 192 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17907) covalent geometry : angle 0.53759 / 0.29 (24328) SS BOND : bond 0.00132 / 0.10 ( 16) SS BOND : angle 0.96379 / 0.61 ( 32) hydrogen bonds : bond 0.04377 / 2.88 ( 837) hydrogen bonds : angle 4.58096 / 3.37 ( 2406) link_BETA1-4 : bond 0.00299 / 0.17 ( 4) link_BETA1-4 : angle 1.05970 / 0.65 ( 12) link_NAG-ASN : bond 0.00222 / 0.16 ( 9) link_NAG-ASN : angle 2.84788 / 2.02 ( 27) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2745.18 seconds wall clock time: 48 minutes 2.27 seconds (2882.27 seconds total)