Starting phenix.real_space_refine on Thu Sep 18 14:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avg_43901/09_2025/9avg_43901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avg_43901/09_2025/9avg_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_43901/09_2025/9avg_43901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avg_43901/09_2025/9avg_43901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9avg_43901/09_2025/9avg_43901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avg_43901/09_2025/9avg_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-2.0-5805/lib/python3.9/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, 64 Unusual residues: {' CA': 3, '9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 80 Unusual residues: {' CA': 3, '9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 4.10, per 1000 atoms: 0.23 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: 1.73 Conformation dependent library (CDL) restraints added in 761.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.64 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: 3.37 Time building geometry restraints manager: 2.20 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: 9.050 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.310 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 aren 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 covalent geometry : bond 0.00499 (17907) covalent geometry : angle 0.69211 (24328) SS BOND : bond 0.00137 ( 16) SS BOND : angle 0.78833 ( 32) hydrogen bonds : bond 0.13694 ( 837) hydrogen bonds : angle 6.14320 ( 2406) link_BETA1-4 : bond 0.00486 ( 4) link_BETA1-4 : angle 1.17892 ( 12) link_NAG-ASN : bond 0.00404 ( 9) link_NAG-ASN : angle 3.05728 ( 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 : 0.594 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: 0.1393 time to fit residues: 79.8269 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 : 0.679 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099019 restraints weight = 28306.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098916 restraints weight = 24184.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099779 restraints weight = 23429.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100238 restraints weight = 19698.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100539 restraints weight = 16502.319| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17936 Z= 0.167 Angle : 0.559 7.873 24399 Z= 0.297 Chirality : 0.043 0.170 2790 Planarity : 0.005 0.056 3056 Dihedral : 7.570 64.867 2791 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.00 % Allowed : 6.71 % Favored : 92.29 % 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 aren not related in a simple way. whole: -0.50 (0.17), residues: 2182 helix: 0.66 (0.16), residues: 918 sheet: -1.49 (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 185 TYR 0.014 0.002 TYR R 421 PHE 0.023 0.002 PHE R 788 TRP 0.012 0.002 TRP Q 299 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00386 (17907) covalent geometry : angle 0.55397 (24328) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.83824 ( 32) hydrogen bonds : bond 0.05025 ( 837) hydrogen bonds : angle 4.99364 ( 2406) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 1.05507 ( 12) link_NAG-ASN : bond 0.00485 ( 9) link_NAG-ASN : angle 2.12506 ( 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 392 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 374 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 261 ASN cc_start: 0.6411 (m110) cc_final: 0.6037 (t0) REVERT: Q 860 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (mt) REVERT: R 248 ASP cc_start: 0.6550 (m-30) cc_final: 0.6134 (m-30) REVERT: R 282 GLU cc_start: 0.6627 (tp30) cc_final: 0.6409 (tp30) REVERT: R 309 GLN cc_start: 0.8062 (pm20) cc_final: 0.7493 (pm20) REVERT: A 122 LEU cc_start: 0.7653 (tp) cc_final: 0.7367 (tp) REVERT: A 234 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 235 ILE cc_start: 0.8713 (mm) cc_final: 0.8398 (mp) REVERT: B 71 VAL cc_start: 0.8538 (m) cc_final: 0.8308 (t) REVERT: B 198 LEU cc_start: 0.8901 (mm) cc_final: 0.8587 (mp) REVERT: B 263 THR cc_start: 0.6945 (m) cc_final: 0.6514 (p) outliers start: 18 outliers final: 13 residues processed: 379 average time/residue: 0.1415 time to fit residues: 80.8105 Evaluate side-chains 361 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 129 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 154 optimal weight: 0.0060 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097992 restraints weight = 28651.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098104 restraints weight = 24418.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099396 restraints weight = 23329.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099753 restraints weight = 17653.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099835 restraints weight = 15579.531| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17936 Z= 0.180 Angle : 0.552 11.439 24399 Z= 0.290 Chirality : 0.043 0.160 2790 Planarity : 0.004 0.048 3056 Dihedral : 7.297 68.940 2791 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 9.43 % Favored : 88.68 % 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 aren not related in a simple way. whole: -0.36 (0.17), residues: 2182 helix: 0.78 (0.16), residues: 920 sheet: -1.39 (0.26), residues: 370 loop : -0.67 (0.20), residues: 892 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 covalent geometry : bond 0.00422 (17907) covalent geometry : angle 0.54646 (24328) SS BOND : bond 0.00405 ( 16) SS BOND : angle 1.05315 ( 32) hydrogen bonds : bond 0.04866 ( 837) hydrogen bonds : angle 4.81687 ( 2406) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 1.09932 ( 12) link_NAG-ASN : bond 0.00653 ( 9) link_NAG-ASN : angle 2.06199 ( 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 395 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 361 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7092 (OUTLIER) cc_final: 0.6740 (t) REVERT: R 248 ASP cc_start: 0.6506 (m-30) cc_final: 0.6166 (m-30) REVERT: R 309 GLN cc_start: 0.8058 (pm20) cc_final: 0.7714 (pm20) REVERT: R 422 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 122 LEU cc_start: 0.7667 (tp) cc_final: 0.7370 (tp) REVERT: A 234 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 36 ASN cc_start: 0.5185 (m-40) cc_final: 0.4865 (p0) REVERT: B 71 VAL cc_start: 0.8479 (m) cc_final: 0.8008 (t) REVERT: B 81 ILE cc_start: 0.8547 (tp) cc_final: 0.8154 (tp) REVERT: B 198 LEU cc_start: 0.8896 (mm) cc_final: 0.8596 (mp) REVERT: B 263 THR cc_start: 0.6970 (m) cc_final: 0.6500 (p) outliers start: 34 outliers final: 20 residues processed: 373 average time/residue: 0.1401 time to fit residues: 78.2816 Evaluate side-chains 366 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 343 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR 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 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 18 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: 0.5980 chunk 171 optimal weight: 0.0060 chunk 78 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098177 restraints weight = 28623.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098298 restraints weight = 24557.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099636 restraints weight = 22082.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099935 restraints weight = 17910.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100059 restraints weight = 15606.636| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17936 Z= 0.165 Angle : 0.536 11.260 24399 Z= 0.280 Chirality : 0.043 0.163 2790 Planarity : 0.004 0.047 3056 Dihedral : 7.021 71.465 2791 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.50 % Allowed : 10.88 % Favored : 86.63 % 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 aren not related in a simple way. whole: -0.30 (0.17), residues: 2182 helix: 0.84 (0.16), residues: 923 sheet: -1.37 (0.26), residues: 370 loop : -0.64 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 314 TYR 0.021 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 covalent geometry : bond 0.00388 (17907) covalent geometry : angle 0.53057 (24328) SS BOND : bond 0.00161 ( 16) SS BOND : angle 1.08243 ( 32) hydrogen bonds : bond 0.04674 ( 837) hydrogen bonds : angle 4.68697 ( 2406) link_BETA1-4 : bond 0.00262 ( 4) link_BETA1-4 : angle 1.05079 ( 12) link_NAG-ASN : bond 0.00463 ( 9) link_NAG-ASN : angle 2.08900 ( 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 402 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 588 ASP cc_start: 0.6631 (t0) cc_final: 0.6416 (t0) REVERT: Q 594 ASN cc_start: 0.6781 (m110) cc_final: 0.6192 (m-40) REVERT: Q 642 ILE cc_start: 0.8703 (mm) cc_final: 0.8453 (mm) REVERT: Q 702 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6712 (t) REVERT: R 248 ASP cc_start: 0.6476 (m-30) cc_final: 0.6131 (m-30) REVERT: R 277 GLU cc_start: 0.7867 (tt0) cc_final: 0.7424 (tt0) REVERT: R 282 GLU cc_start: 0.6618 (tp30) cc_final: 0.6383 (tp30) REVERT: R 309 GLN cc_start: 0.8092 (pm20) cc_final: 0.7718 (pm20) REVERT: R 422 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 106 ILE cc_start: 0.8260 (mm) cc_final: 0.7979 (mm) REVERT: A 122 LEU cc_start: 0.7664 (tp) cc_final: 0.7358 (tp) REVERT: A 234 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 235 ILE cc_start: 0.8671 (mm) cc_final: 0.8440 (mp) REVERT: B 36 ASN cc_start: 0.5210 (m-40) cc_final: 0.4881 (p0) REVERT: B 198 LEU cc_start: 0.8880 (mm) cc_final: 0.8591 (mp) REVERT: B 314 ARG cc_start: 0.8302 (mtm110) cc_final: 0.7914 (mtp-110) outliers start: 45 outliers final: 29 residues processed: 381 average time/residue: 0.1313 time to fit residues: 75.3750 Evaluate side-chains 370 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 234 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 102 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 124 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098415 restraints weight = 28329.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098634 restraints weight = 24829.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099295 restraints weight = 25146.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099866 restraints weight = 19333.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100072 restraints weight = 16626.369| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17936 Z= 0.169 Angle : 0.535 9.873 24399 Z= 0.281 Chirality : 0.043 0.211 2790 Planarity : 0.004 0.051 3056 Dihedral : 6.847 72.212 2791 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.33 % Allowed : 12.26 % Favored : 85.41 % 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 aren not related in a simple way. whole: -0.21 (0.17), residues: 2182 helix: 0.91 (0.16), residues: 922 sheet: -1.29 (0.26), residues: 364 loop : -0.63 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 535 TYR 0.021 0.002 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 Q 466 Details of bonding type rmsd covalent geometry : bond 0.00397 (17907) covalent geometry : angle 0.52831 (24328) SS BOND : bond 0.00347 ( 16) SS BOND : angle 0.88268 ( 32) hydrogen bonds : bond 0.04643 ( 837) hydrogen bonds : angle 4.64188 ( 2406) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 1.06087 ( 12) link_NAG-ASN : bond 0.00334 ( 9) link_NAG-ASN : angle 2.38375 ( 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: 42 poor density : 359 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6695 (t) REVERT: R 248 ASP cc_start: 0.6519 (m-30) cc_final: 0.6180 (m-30) REVERT: R 277 GLU cc_start: 0.7872 (tt0) cc_final: 0.7402 (tt0) REVERT: R 309 GLN cc_start: 0.8085 (pm20) cc_final: 0.7708 (pm20) REVERT: R 422 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7667 (mp) REVERT: R 526 GLU cc_start: 0.6693 (pp20) cc_final: 0.6405 (pp20) REVERT: A 106 ILE cc_start: 0.8334 (mm) cc_final: 0.7948 (mm) REVERT: A 122 LEU cc_start: 0.7669 (tp) cc_final: 0.7370 (tp) REVERT: A 234 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 36 ASN cc_start: 0.5189 (m-40) cc_final: 0.4873 (p0) REVERT: B 198 LEU cc_start: 0.8868 (mm) cc_final: 0.8606 (mp) REVERT: B 314 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7900 (mtp-110) outliers start: 42 outliers final: 28 residues processed: 380 average time/residue: 0.1442 time to fit residues: 82.1914 Evaluate side-chains 372 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 341 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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 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 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 33 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097375 restraints weight = 28394.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097258 restraints weight = 22045.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097814 restraints weight = 21044.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098320 restraints weight = 17929.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098414 restraints weight = 15207.636| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17936 Z= 0.207 Angle : 0.563 11.956 24399 Z= 0.295 Chirality : 0.044 0.146 2790 Planarity : 0.004 0.053 3056 Dihedral : 6.859 73.605 2791 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.77 % Allowed : 13.49 % Favored : 83.74 % 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 aren not related in a simple way. whole: -0.28 (0.17), residues: 2182 helix: 0.85 (0.16), residues: 921 sheet: -1.30 (0.26), residues: 361 loop : -0.68 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 135 TYR 0.022 0.002 TYR R 744 PHE 0.022 0.002 PHE A 100 TRP 0.014 0.002 TRP Q 299 HIS 0.005 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00493 (17907) covalent geometry : angle 0.55537 (24328) SS BOND : bond 0.00242 ( 16) SS BOND : angle 1.09996 ( 32) hydrogen bonds : bond 0.04806 ( 837) hydrogen bonds : angle 4.68217 ( 2406) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 1.10445 ( 12) link_NAG-ASN : bond 0.00410 ( 9) link_NAG-ASN : angle 2.50404 ( 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 410 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6694 (t) REVERT: R 248 ASP cc_start: 0.6559 (m-30) cc_final: 0.6210 (m-30) REVERT: R 309 GLN cc_start: 0.8085 (pm20) cc_final: 0.7697 (pm20) REVERT: R 422 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7660 (mp) REVERT: R 526 GLU cc_start: 0.6736 (pp20) cc_final: 0.6451 (pp20) REVERT: A 106 ILE cc_start: 0.8339 (mm) cc_final: 0.7986 (mm) REVERT: A 122 LEU cc_start: 0.7783 (tp) cc_final: 0.7484 (tp) REVERT: A 234 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8659 (mp) REVERT: A 235 ILE cc_start: 0.8678 (mm) cc_final: 0.8452 (mp) REVERT: B 36 ASN cc_start: 0.5222 (m-40) cc_final: 0.4885 (p0) REVERT: B 198 LEU cc_start: 0.8917 (mm) cc_final: 0.8659 (mp) REVERT: B 314 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7941 (mtp-110) outliers start: 50 outliers final: 36 residues processed: 386 average time/residue: 0.1424 time to fit residues: 82.1910 Evaluate side-chains 388 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 252 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 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 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 37 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 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 157 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 215 optimal weight: 0.9980 chunk 188 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 146 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098086 restraints weight = 28529.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097896 restraints weight = 22783.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098620 restraints weight = 21561.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099072 restraints weight = 17853.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099155 restraints weight = 15490.273| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17936 Z= 0.158 Angle : 0.555 11.234 24399 Z= 0.286 Chirality : 0.043 0.144 2790 Planarity : 0.004 0.054 3056 Dihedral : 6.726 73.271 2791 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.83 % Allowed : 13.82 % Favored : 83.35 % 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 aren not related in a simple way. whole: -0.15 (0.17), residues: 2182 helix: 0.99 (0.16), residues: 921 sheet: -1.23 (0.26), residues: 370 loop : -0.62 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.021 0.002 TYR R 744 PHE 0.026 0.002 PHE A 100 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00370 (17907) covalent geometry : angle 0.53850 (24328) SS BOND : bond 0.00251 ( 16) SS BOND : angle 0.98571 ( 32) hydrogen bonds : bond 0.04576 ( 837) hydrogen bonds : angle 4.62158 ( 2406) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.04171 ( 12) link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 3.92022 ( 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 408 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: Q 561 CYS cc_start: 0.5008 (m) cc_final: 0.4785 (m) REVERT: R 216 ASP cc_start: 0.7189 (p0) cc_final: 0.6949 (p0) REVERT: R 248 ASP cc_start: 0.6551 (m-30) cc_final: 0.6187 (m-30) REVERT: R 277 GLU cc_start: 0.7882 (tt0) cc_final: 0.7430 (tt0) REVERT: R 282 GLU cc_start: 0.6730 (tp30) cc_final: 0.6318 (tp30) REVERT: R 309 GLN cc_start: 0.8120 (pm20) cc_final: 0.7731 (pm20) REVERT: R 422 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7662 (mp) REVERT: R 526 GLU cc_start: 0.6698 (pp20) cc_final: 0.6389 (pp20) REVERT: R 795 ARG cc_start: 0.7582 (ptt-90) cc_final: 0.7292 (ptt-90) REVERT: A 122 LEU cc_start: 0.7752 (tp) cc_final: 0.7461 (tp) REVERT: A 234 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 235 ILE cc_start: 0.8677 (mm) cc_final: 0.8463 (mp) REVERT: B 36 ASN cc_start: 0.5220 (m-40) cc_final: 0.4919 (p0) REVERT: B 155 ASN cc_start: 0.7131 (t0) cc_final: 0.6890 (t0) REVERT: B 198 LEU cc_start: 0.8895 (mm) cc_final: 0.8648 (mp) REVERT: B 285 LEU cc_start: 0.8909 (tp) cc_final: 0.8494 (tt) REVERT: B 314 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7917 (mtp-110) outliers start: 51 outliers final: 35 residues processed: 386 average time/residue: 0.1294 time to fit residues: 75.3314 Evaluate side-chains 378 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 38 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 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 270 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: 0.4980 chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097001 restraints weight = 28475.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096766 restraints weight = 23703.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097685 restraints weight = 22304.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098241 restraints weight = 19186.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098255 restraints weight = 16949.516| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17936 Z= 0.236 Angle : 0.606 11.283 24399 Z= 0.315 Chirality : 0.045 0.157 2790 Planarity : 0.004 0.057 3056 Dihedral : 6.879 74.333 2791 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.55 % Allowed : 14.93 % Favored : 82.52 % 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 aren not related in a simple way. whole: -0.32 (0.17), residues: 2182 helix: 0.83 (0.16), residues: 920 sheet: -1.32 (0.26), residues: 365 loop : -0.70 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 185 TYR 0.024 0.002 TYR Q 510 PHE 0.025 0.002 PHE R 444 TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00564 (17907) covalent geometry : angle 0.59493 (24328) SS BOND : bond 0.00306 ( 16) SS BOND : angle 1.62104 ( 32) hydrogen bonds : bond 0.04946 ( 837) hydrogen bonds : angle 4.74740 ( 2406) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.13570 ( 12) link_NAG-ASN : bond 0.00524 ( 9) link_NAG-ASN : angle 3.09124 ( 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 396 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: Q 561 CYS cc_start: 0.5026 (m) cc_final: 0.4807 (m) REVERT: R 216 ASP cc_start: 0.7223 (p0) cc_final: 0.6995 (p0) REVERT: R 248 ASP cc_start: 0.6544 (m-30) cc_final: 0.6202 (m-30) REVERT: R 309 GLN cc_start: 0.8105 (pm20) cc_final: 0.7652 (pm20) REVERT: R 422 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 106 ILE cc_start: 0.7894 (mm) cc_final: 0.7644 (mm) REVERT: A 122 LEU cc_start: 0.7730 (tp) cc_final: 0.7439 (tp) REVERT: A 235 ILE cc_start: 0.8662 (mm) cc_final: 0.8431 (mp) REVERT: B 36 ASN cc_start: 0.5204 (m-40) cc_final: 0.4905 (p0) REVERT: B 155 ASN cc_start: 0.7155 (t0) cc_final: 0.6915 (t0) REVERT: B 198 LEU cc_start: 0.8921 (mm) cc_final: 0.8656 (mp) REVERT: B 285 LEU cc_start: 0.8910 (tp) cc_final: 0.8499 (tt) REVERT: B 311 HIS cc_start: 0.6542 (m-70) cc_final: 0.6086 (t-90) REVERT: B 314 ARG cc_start: 0.8302 (mtm110) cc_final: 0.7931 (mtp-110) outliers start: 46 outliers final: 38 residues processed: 377 average time/residue: 0.1310 time to fit residues: 74.2545 Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 252 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 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 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 37 LEU Chi-restraints excluded: chain A residue 124 ASP 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 270 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: 0.2980 chunk 91 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 156 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098384 restraints weight = 28449.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098436 restraints weight = 24038.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099158 restraints weight = 24719.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099591 restraints weight = 19270.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099903 restraints weight = 16624.392| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17936 Z= 0.141 Angle : 0.568 15.817 24399 Z= 0.294 Chirality : 0.043 0.176 2790 Planarity : 0.004 0.063 3056 Dihedral : 6.662 73.650 2791 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.13 % 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 aren not related in a simple way. whole: -0.18 (0.17), residues: 2182 helix: 0.97 (0.16), residues: 924 sheet: -1.31 (0.25), residues: 373 loop : -0.62 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.023 0.002 TYR Q 510 PHE 0.018 0.001 PHE Q 637 TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00327 (17907) covalent geometry : angle 0.55855 (24328) SS BOND : bond 0.00264 ( 16) SS BOND : angle 1.17835 ( 32) hydrogen bonds : bond 0.04529 ( 837) hydrogen bonds : angle 4.64009 ( 2406) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 1.03599 ( 12) link_NAG-ASN : bond 0.00291 ( 9) link_NAG-ASN : angle 2.86901 ( 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 384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: Q 335 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7312 (mmtp) REVERT: Q 510 TYR cc_start: 0.7988 (p90) cc_final: 0.7767 (p90) REVERT: Q 561 CYS cc_start: 0.4975 (m) cc_final: 0.4753 (m) REVERT: R 216 ASP cc_start: 0.7198 (p0) cc_final: 0.6979 (p0) REVERT: R 248 ASP cc_start: 0.6543 (m-30) cc_final: 0.6184 (m-30) REVERT: R 277 GLU cc_start: 0.7878 (tt0) cc_final: 0.7400 (tt0) REVERT: R 309 GLN cc_start: 0.8106 (pm20) cc_final: 0.7635 (pm20) REVERT: R 422 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7710 (mp) REVERT: R 592 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7691 (p0) REVERT: R 795 ARG cc_start: 0.7600 (ptt-90) cc_final: 0.7342 (ptt-90) REVERT: A 122 LEU cc_start: 0.7684 (tp) cc_final: 0.7392 (tp) REVERT: B 198 LEU cc_start: 0.8896 (mm) cc_final: 0.8611 (mp) REVERT: B 285 LEU cc_start: 0.8905 (tp) cc_final: 0.8488 (tt) REVERT: B 314 ARG cc_start: 0.8269 (mtm110) cc_final: 0.7866 (mtp-110) outliers start: 40 outliers final: 32 residues processed: 364 average time/residue: 0.1388 time to fit residues: 76.2346 Evaluate side-chains 374 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 339 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 422 LEU Chi-restraints excluded: chain R residue 478 THR 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 37 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 171 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 270 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: 0.9990 chunk 101 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 134 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097905 restraints weight = 28109.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098158 restraints weight = 22666.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099014 restraints weight = 21618.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099359 restraints weight = 17857.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099656 restraints weight = 14976.944| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17936 Z= 0.181 Angle : 0.582 13.750 24399 Z= 0.302 Chirality : 0.043 0.152 2790 Planarity : 0.004 0.068 3056 Dihedral : 6.677 73.150 2791 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.00 % Allowed : 16.15 % Favored : 81.85 % 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 aren not related in a simple way. whole: -0.20 (0.17), residues: 2182 helix: 0.92 (0.16), residues: 926 sheet: -1.24 (0.26), residues: 366 loop : -0.65 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.023 0.002 TYR Q 510 PHE 0.023 0.002 PHE Q 637 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00431 (17907) covalent geometry : angle 0.57443 (24328) SS BOND : bond 0.00190 ( 16) SS BOND : angle 1.12651 ( 32) hydrogen bonds : bond 0.04666 ( 837) hydrogen bonds : angle 4.66577 ( 2406) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 1.07917 ( 12) link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 2.66921 ( 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 383 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: Q 228 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6177 (mt-10) REVERT: Q 270 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: Q 335 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7298 (mmtp) REVERT: Q 561 CYS cc_start: 0.5002 (m) cc_final: 0.4781 (m) REVERT: Q 564 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.6012 (pt0) REVERT: R 216 ASP cc_start: 0.7187 (p0) cc_final: 0.6964 (p0) REVERT: R 248 ASP cc_start: 0.6566 (m-30) cc_final: 0.6208 (m-30) REVERT: R 277 GLU cc_start: 0.7893 (tt0) cc_final: 0.7436 (tt0) REVERT: R 282 GLU cc_start: 0.6771 (tp30) cc_final: 0.6380 (tp30) REVERT: R 309 GLN cc_start: 0.8105 (pm20) cc_final: 0.7697 (pm20) REVERT: R 422 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7673 (mp) REVERT: R 526 GLU cc_start: 0.6743 (pp20) cc_final: 0.6466 (pp20) REVERT: R 795 ARG cc_start: 0.7610 (ptt-90) cc_final: 0.7327 (ptt-90) REVERT: A 122 LEU cc_start: 0.7708 (tp) cc_final: 0.7422 (tp) REVERT: A 235 ILE cc_start: 0.8631 (mm) cc_final: 0.8422 (mp) REVERT: B 36 ASN cc_start: 0.5169 (m-40) cc_final: 0.4954 (p0) REVERT: B 155 ASN cc_start: 0.7099 (t0) cc_final: 0.6865 (t0) REVERT: B 198 LEU cc_start: 0.8911 (mm) cc_final: 0.8627 (mp) REVERT: B 285 LEU cc_start: 0.8893 (tp) cc_final: 0.8475 (tt) REVERT: B 311 HIS cc_start: 0.6453 (m-70) cc_final: 0.6142 (t-90) REVERT: B 314 ARG cc_start: 0.8283 (mtm110) cc_final: 0.7924 (mtp-110) outliers start: 36 outliers final: 32 residues processed: 366 average time/residue: 0.1462 time to fit residues: 80.6968 Evaluate side-chains 368 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 564 GLU 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 24 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU 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 37 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 171 ILE 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 270 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: 0.0970 chunk 148 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097284 restraints weight = 28582.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097455 restraints weight = 22789.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098208 restraints weight = 22390.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098654 restraints weight = 18012.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098775 restraints weight = 15849.694| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17936 Z= 0.206 Angle : 0.596 13.717 24399 Z= 0.310 Chirality : 0.044 0.148 2790 Planarity : 0.004 0.071 3056 Dihedral : 6.737 73.761 2791 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.22 % Allowed : 15.98 % Favored : 81.80 % 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 aren not related in a simple way. whole: -0.26 (0.17), residues: 2182 helix: 0.85 (0.16), residues: 926 sheet: -1.18 (0.26), residues: 363 loop : -0.69 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.019 0.002 TYR R 744 PHE 0.028 0.002 PHE A 100 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS Q 466 Details of bonding type rmsd covalent geometry : bond 0.00491 (17907) covalent geometry : angle 0.58886 (24328) SS BOND : bond 0.00219 ( 16) SS BOND : angle 1.12570 ( 32) hydrogen bonds : bond 0.04772 ( 837) hydrogen bonds : angle 4.71831 ( 2406) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 1.10406 ( 12) link_NAG-ASN : bond 0.00410 ( 9) link_NAG-ASN : angle 2.56265 ( 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: 2755.04 seconds wall clock time: 48 minutes 9.65 seconds (2889.65 seconds total)