Starting phenix.real_space_refine on Sun Jul 5 06:56:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694.map" model { file = "/net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abf_11694/07_2026/7abf_11694_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 161 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 15892 2.51 5 N 4756 2.21 5 O 5054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25904 Number of models: 1 Model: "" Number of chains: 17 Chain: "Q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 850 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 12, 'ASP:plan': 3, 'GLU:plan': 12, 'GLN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1151 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 9, 'HIS:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 17, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 181 Chain: "A" Number of atoms: 10522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1656, 10522 Classifications: {'peptide': 1656} Incomplete info: {'truncation_to_alanine': 958} Link IDs: {'PTRANS': 91, 'TRANS': 1564} Chain breaks: 2 Unresolved non-hydrogen bonds: 3415 Unresolved non-hydrogen angles: 4325 Unresolved non-hydrogen dihedrals: 2744 Unresolved non-hydrogen chiralities: 297 Planarities with less than four sites: {'GLU:plan': 90, 'ARG:plan': 80, 'HIS:plan': 25, 'ASP:plan': 94, 'ASN:plan1': 72, 'PHE:plan': 24, 'TYR:plan': 26, 'GLN:plan1': 56, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 2014 Chain: "r" Number of atoms: 5120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 5120 Classifications: {'peptide': 844} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 49, 'TRANS': 794} Unresolved non-hydrogen bonds: 1585 Unresolved non-hydrogen angles: 2002 Unresolved non-hydrogen dihedrals: 1263 Unresolved non-hydrogen chiralities: 150 Planarities with less than four sites: {'TYR:plan': 8, 'GLU:plan': 54, 'ASP:plan': 55, 'ASN:plan1': 19, 'ARG:plan': 27, 'GLN:plan1': 23, 'HIS:plan': 7, 'PHE:plan': 18, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 891 Chain: "N" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 295 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 523 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "5" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1220 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 46} Chain: "6" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1392 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 52} Chain breaks: 1 Chain: "X" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 182 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "v" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1604 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 13, 'TRANS': 306} Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1264 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 10, 'TRP:plan': 11, 'HIS:plan': 17, 'TYR:plan': 8, 'ARG:plan': 18, 'GLU:plan': 10, 'ASN:plan1': 11, 'PHE:plan': 8, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 551 Chain: "Z" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 622 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 799 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 19, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 9, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "A4" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1235 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PTRANS': 2, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 904 Unresolved non-hydrogen angles: 1121 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 37, 'ARG:plan': 31, 'GLN:plan1': 12, 'PHE:plan': 8, 'ASP:plan': 18, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 551 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.06, per 1000 atoms: 0.23 Number of scatterers: 25904 At special positions: 0 Unit cell: (168.2, 160.08, 168.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 161 15.00 Mg 1 11.99 O 5054 8.00 N 4756 7.00 C 15892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 32 sheets defined 44.9% alpha, 7.7% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'Q' and resid 12 through 16 removed outlier: 3.676A pdb=" N TRP Q 15 " --> pdb=" O PRO Q 12 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU Q 16 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 12 through 16' Processing helix chain 'Q' and resid 18 through 34 Processing helix chain 'Q' and resid 43 through 45 No H-bonds generated for 'chain 'Q' and resid 43 through 45' Processing helix chain 'Q' and resid 46 through 65 removed outlier: 3.931A pdb=" N PHE Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 81 removed outlier: 5.309A pdb=" N ILE Q 79 " --> pdb=" O TYR Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 94 removed outlier: 3.967A pdb=" N LYS Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.694A pdb=" N ASP I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 83 through 92 removed outlier: 3.601A pdb=" N ILE I 87 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 Processing helix chain 'I' and resid 112 through 121 Processing helix chain 'I' and resid 122 through 124 No H-bonds generated for 'chain 'I' and resid 122 through 124' Processing helix chain 'I' and resid 144 through 153 Processing helix chain 'I' and resid 167 through 175 removed outlier: 3.805A pdb=" N LEU I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.951A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.648A pdb=" N MET A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.501A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.227A pdb=" N TYR A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.811A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.513A pdb=" N ARG A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 511 Processing helix chain 'A' and resid 543 through 566 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.390A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 661 Proline residue: A 646 - end of helix removed outlier: 4.043A pdb=" N ALA A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 769 through 797 removed outlier: 4.129A pdb=" N LYS A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 859 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1002 through 1014 removed outlier: 3.812A pdb=" N ASN A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.889A pdb=" N ILE A1040 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1076 through 1082 removed outlier: 4.127A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.910A pdb=" N ASN A1148 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1249 Processing helix chain 'A' and resid 1255 through 1271 Processing helix chain 'A' and resid 1275 through 1281 removed outlier: 3.782A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1300 removed outlier: 4.728A pdb=" N ARG A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.663A pdb=" N THR A1318 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.865A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1400 removed outlier: 4.353A pdb=" N ALA A1387 " --> pdb=" O GLN A1383 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A1388 " --> pdb=" O ARG A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 Processing helix chain 'A' and resid 1418 through 1423 removed outlier: 3.866A pdb=" N LEU A1422 " --> pdb=" O ARG A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.834A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1443 Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1485 Processing helix chain 'A' and resid 1529 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 removed outlier: 3.530A pdb=" N LYS A1584 " --> pdb=" O HIS A1580 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1674 removed outlier: 3.962A pdb=" N HIS A1674 " --> pdb=" O TYR A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1690 removed outlier: 3.570A pdb=" N TYR A1679 " --> pdb=" O ASP A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1735 removed outlier: 3.630A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'r' and resid 115 through 124 Processing helix chain 'r' and resid 142 through 154 Processing helix chain 'r' and resid 172 through 178 Processing helix chain 'r' and resid 208 through 219 Processing helix chain 'r' and resid 236 through 250 removed outlier: 4.300A pdb=" N LYS r 244 " --> pdb=" O GLU r 240 " (cutoff:3.500A) Processing helix chain 'r' and resid 260 through 265 Processing helix chain 'r' and resid 270 through 293 Processing helix chain 'r' and resid 319 through 332 removed outlier: 3.897A pdb=" N GLY r 332 " --> pdb=" O ALA r 328 " (cutoff:3.500A) Processing helix chain 'r' and resid 335 through 340 removed outlier: 3.876A pdb=" N PHE r 339 " --> pdb=" O ASN r 335 " (cutoff:3.500A) Processing helix chain 'r' and resid 367 through 373 Processing helix chain 'r' and resid 373 through 386 Processing helix chain 'r' and resid 390 through 400 removed outlier: 4.705A pdb=" N ARG r 394 " --> pdb=" O THR r 390 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU r 398 " --> pdb=" O ARG r 394 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU r 399 " --> pdb=" O THR r 395 " (cutoff:3.500A) Processing helix chain 'r' and resid 406 through 410 removed outlier: 3.836A pdb=" N LEU r 410 " --> pdb=" O GLU r 407 " (cutoff:3.500A) Processing helix chain 'r' and resid 411 through 424 Processing helix chain 'r' and resid 430 through 435 Processing helix chain 'r' and resid 440 through 453 removed outlier: 5.107A pdb=" N LYS r 446 " --> pdb=" O LYS r 442 " (cutoff:3.500A) Proline residue: r 447 - end of helix Processing helix chain 'r' and resid 459 through 466 Processing helix chain 'r' and resid 599 through 614 Processing helix chain 'r' and resid 633 through 647 Processing helix chain 'r' and resid 693 through 702 Processing helix chain 'r' and resid 710 through 721 Processing helix chain 'r' and resid 725 through 731 Processing helix chain 'r' and resid 736 through 740 Processing helix chain 'r' and resid 755 through 762 removed outlier: 3.545A pdb=" N LEU r 759 " --> pdb=" O ASP r 755 " (cutoff:3.500A) Processing helix chain 'r' and resid 762 through 775 removed outlier: 3.742A pdb=" N ILE r 766 " --> pdb=" O VAL r 762 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG r 775 " --> pdb=" O GLN r 771 " (cutoff:3.500A) Processing helix chain 'r' and resid 804 through 807 removed outlier: 3.510A pdb=" N GLN r 807 " --> pdb=" O GLY r 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 804 through 807' Processing helix chain 'r' and resid 808 through 822 Processing helix chain 'r' and resid 839 through 853 Processing helix chain 'r' and resid 882 through 891 removed outlier: 3.536A pdb=" N HIS r 890 " --> pdb=" O ASP r 886 " (cutoff:3.500A) Processing helix chain 'r' and resid 928 through 942 Processing helix chain 'r' and resid 948 through 953 removed outlier: 4.233A pdb=" N PHE r 952 " --> pdb=" O SER r 948 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 100 removed outlier: 4.058A pdb=" N HIS N 98 " --> pdb=" O ASN N 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 109 removed outlier: 3.615A pdb=" N GLY N 109 " --> pdb=" O GLN N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 removed outlier: 3.927A pdb=" N GLN N 121 " --> pdb=" O SER N 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 122 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL N 128 " --> pdb=" O LYS N 124 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 36 Processing helix chain 'q' and resid 56 through 61 removed outlier: 4.066A pdb=" N TYR q 60 " --> pdb=" O SER q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 225 Processing helix chain 'X' and resid 25 through 48 removed outlier: 3.723A pdb=" N LYS X 48 " --> pdb=" O VAL X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 58 removed outlier: 3.652A pdb=" N GLU X 58 " --> pdb=" O ILE X 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 138 through 159 Processing helix chain 'v' and resid 283 through 313 Processing helix chain 'K' and resid 272 through 314 removed outlier: 3.563A pdb=" N GLU K 277 " --> pdb=" O GLU K 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS K 280 " --> pdb=" O TYR K 276 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing helix chain 'A4' and resid 700 through 721 Processing helix chain 'A4' and resid 857 through 891 Processing helix chain 'A4' and resid 897 through 910 Processing helix chain 'A4' and resid 917 through 926 Processing helix chain 'A4' and resid 930 through 935 removed outlier: 3.694A pdb=" N GLYA4 934 " --> pdb=" O TRPA4 931 " (cutoff:3.500A) Processing helix chain 'A4' and resid 938 through 967 Processing helix chain 'A4' and resid 976 through 981 Processing helix chain 'A4' and resid 982 through 987 removed outlier: 4.426A pdb=" N GLUA4 986 " --> pdb=" O LYSA4 982 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASPA4 987 " --> pdb=" O ILEA4 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 982 through 987' Processing helix chain 'A4' and resid 987 through 992 removed outlier: 3.912A pdb=" N ILEA4 991 " --> pdb=" O ASPA4 987 " (cutoff:3.500A) Processing helix chain 'A4' and resid 996 through 1025 Processing helix chain 'A4' and resid 1031 through 1040 removed outlier: 4.275A pdb=" N LYSA41035 " --> pdb=" O TYRA41031 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SERA41040 " --> pdb=" O LEUA41036 " (cutoff:3.500A) Processing helix chain 'A4' and resid 1041 through 1051 removed outlier: 3.617A pdb=" N LYSA41045 " --> pdb=" O ASPA41041 " (cutoff:3.500A) Processing helix chain 'A4' and resid 1054 through 1060 Processing helix chain 'A4' and resid 1063 through 1080 Processing sheet with id=AA1, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'I' and resid 129 through 133 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 517 Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 898 Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 4.823A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 975 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1101 " --> pdb=" O CYS A 973 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 973 " --> pdb=" O PHE A1101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id=AA8, first strand: chain 'A' and resid 1215 through 1217 removed outlier: 6.610A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1334 through 1335 removed outlier: 3.616A pdb=" N ASP A1362 " --> pdb=" O ILE A1335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1341 through 1342 Processing sheet with id=AB2, first strand: chain 'A' and resid 1553 through 1554 removed outlier: 3.657A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 6.891A pdb=" N PHE A1632 " --> pdb=" O GLU A1607 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A1609 " --> pdb=" O LEU A1630 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A1630 " --> pdb=" O VAL A1609 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1640 through 1644 removed outlier: 3.768A pdb=" N TRP A1718 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY A1716 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1665 through 1667 Processing sheet with id=AB6, first strand: chain 'r' and resid 185 through 190 removed outlier: 3.634A pdb=" N PHE r 200 " --> pdb=" O VAL r 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU r 190 " --> pdb=" O TYR r 198 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR r 198 " --> pdb=" O LEU r 190 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN r 131 " --> pdb=" O GLY r 224 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL r 226 " --> pdb=" O ASN r 131 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR r 133 " --> pdb=" O VAL r 226 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE r 228 " --> pdb=" O THR r 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'r' and resid 348 through 350 Processing sheet with id=AB8, first strand: chain 'r' and resid 475 through 482 removed outlier: 7.432A pdb=" N CYS r 476 " --> pdb=" O LEU r 497 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU r 497 " --> pdb=" O CYS r 476 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR r 478 " --> pdb=" O ARG r 495 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG r 495 " --> pdb=" O THR r 478 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS r 480 " --> pdb=" O PHE r 493 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY r 494 " --> pdb=" O VAL r 550 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL r 550 " --> pdb=" O GLY r 494 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN r 548 " --> pdb=" O VAL r 496 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'r' and resid 501 through 502 Processing sheet with id=AC1, first strand: chain 'r' and resid 523 through 526 removed outlier: 3.518A pdb=" N THR r 566 " --> pdb=" O LYS r 508 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR r 564 " --> pdb=" O LEU r 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'r' and resid 620 through 621 removed outlier: 3.551A pdb=" N LYS r 620 " --> pdb=" O VAL r 628 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'r' and resid 783 through 784 removed outlier: 3.549A pdb=" N CYS r 663 " --> pdb=" O MET r 828 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE r 875 " --> pdb=" O TYR r 832 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU r 868 " --> pdb=" O ILE r 863 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE r 874 " --> pdb=" O VAL r 857 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL r 857 " --> pdb=" O PHE r 874 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'r' and resid 783 through 784 removed outlier: 3.549A pdb=" N CYS r 663 " --> pdb=" O MET r 828 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'r' and resid 674 through 677 removed outlier: 4.125A pdb=" N CYS r 674 " --> pdb=" O MET r 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET r 687 " --> pdb=" O CYS r 674 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS r 684 " --> pdb=" O ALA r 794 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA r 794 " --> pdb=" O LYS r 684 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR r 686 " --> pdb=" O LEU r 792 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA r 734 " --> pdb=" O LEU r 745 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP r 747 " --> pdb=" O ILE r 732 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE r 732 " --> pdb=" O ASP r 747 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 80 through 81 Processing sheet with id=AC7, first strand: chain 'q' and resid 14 through 16 removed outlier: 7.008A pdb=" N VAL q 5 " --> pdb=" O LEU q 68 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU q 70 " --> pdb=" O VAL q 5 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN q 7 " --> pdb=" O LEU q 70 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N TYR q 72 " --> pdb=" O ASN q 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 194 through 199 removed outlier: 6.419A pdb=" N VAL G 488 " --> pdb=" O TYR G 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 210 through 212 Processing sheet with id=AD1, first strand: chain 'G' and resid 251 through 254 Processing sheet with id=AD2, first strand: chain 'G' and resid 291 through 296 removed outlier: 4.178A pdb=" N GLY G 293 " --> pdb=" O CYS G 306 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 336 through 337 removed outlier: 3.719A pdb=" N ILE G 346 " --> pdb=" O ARG G 337 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AD5, first strand: chain 'G' and resid 416 through 419 removed outlier: 6.720A pdb=" N GLY G 430 " --> pdb=" O ASN G 417 " (cutoff:3.500A) 1259 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.10 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6635 1.33 - 1.45: 5596 1.45 - 1.57: 14157 1.57 - 1.69: 311 1.69 - 1.81: 73 Bond restraints: 26772 Sorted by residual: bond pdb=" C GLY r 141 " pdb=" N LYS r 142 " ideal model delta sigma weight residual 1.333 1.406 -0.073 1.34e-02 5.57e+03 2.97e+01 bond pdb=" C GLY r 141 " pdb=" O GLY r 141 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.35e-02 5.49e+03 1.49e+01 bond pdb=" N LYS K 390 " pdb=" CA LYS K 390 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.15e+01 bond pdb=" N VAL G 379 " pdb=" CA VAL G 379 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.21e-02 6.83e+03 8.74e+00 bond pdb=" N VAL K 380 " pdb=" CA VAL K 380 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 26767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 37544 4.00 - 8.00: 157 8.00 - 11.99: 12 11.99 - 15.99: 1 15.99 - 19.99: 2 Bond angle restraints: 37716 Sorted by residual: angle pdb=" C GLY r 141 " pdb=" N LYS r 142 " pdb=" CA LYS r 142 " ideal model delta sigma weight residual 122.17 103.76 18.41 1.54e+00 4.22e-01 1.43e+02 angle pdb=" PA GTP r1500 " pdb=" O3A GTP r1500 " pdb=" PB GTP r1500 " ideal model delta sigma weight residual 120.50 140.49 -19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" CA GLY r 141 " pdb=" C GLY r 141 " pdb=" O GLY r 141 " ideal model delta sigma weight residual 120.57 109.05 11.52 1.74e+00 3.30e-01 4.39e+01 angle pdb=" PB GTP r1500 " pdb=" O3B GTP r1500 " pdb=" PG GTP r1500 " ideal model delta sigma weight residual 120.50 136.20 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C2 C 6 66 " pdb=" N1 C 6 66 " pdb=" C6 C 6 66 " ideal model delta sigma weight residual 120.30 118.24 2.06 4.00e-01 6.25e+00 2.66e+01 ... (remaining 37711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15359 35.89 - 71.78: 350 71.78 - 107.68: 56 107.68 - 143.57: 7 143.57 - 179.46: 3 Dihedral angle restraints: 15775 sinusoidal: 4851 harmonic: 10924 Sorted by residual: dihedral pdb=" O4' C 5 23 " pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sinusoidal sigma weight residual 200.00 45.55 154.45 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" O4' C 6 37 " pdb=" C1' C 6 37 " pdb=" N1 C 6 37 " pdb=" C2 C 6 37 " ideal model delta sinusoidal sigma weight residual -128.00 51.46 -179.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' GTP r1500 " pdb=" O5' GTP r1500 " pdb=" PA GTP r1500 " pdb=" O3A GTP r1500 " ideal model delta sinusoidal sigma weight residual 69.27 -168.03 -122.70 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 15772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 4672 1.006 - 2.011: 0 2.011 - 3.017: 0 3.017 - 4.023: 0 4.023 - 5.028: 3 Chirality restraints: 4675 Sorted by residual: chirality pdb=" C4 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" C5 IHP A3001 " pdb=" O14 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.48 -2.55 5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.29 -4.81 2.00e-01 2.50e+01 5.78e+02 chirality pdb=" C1 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O11 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.32 -2.47 4.78 2.00e-01 2.50e+01 5.72e+02 ... (remaining 4672 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 167 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 168 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 108 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO A 109 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 946 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 947 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 947 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 947 " 0.030 5.00e-02 4.00e+02 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 44 2.38 - 3.01: 14103 3.01 - 3.64: 39454 3.64 - 4.27: 51457 4.27 - 4.90: 82342 Nonbonded interactions: 187400 Sorted by model distance: nonbonded pdb=" N1 G 5 24 " pdb=" N3 G 5 57 " model vdw 1.747 3.200 nonbonded pdb=" N2 G 5 24 " pdb=" O2' G 5 57 " model vdw 1.860 3.120 nonbonded pdb=" O GLY r 141 " pdb=" CD2 PHE r 228 " model vdw 1.972 3.340 nonbonded pdb=" N GLN r 313 " pdb=" N2 GTP r1500 " model vdw 1.980 2.560 nonbonded pdb=" C6 G 5 24 " pdb=" N3 G 5 57 " model vdw 2.052 3.340 ... (remaining 187395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.004 0.163 26774 Z= 0.230 Angle : 0.692 19.992 37716 Z= 0.393 Chirality : 0.130 5.028 4675 Planarity : 0.004 0.067 4463 Dihedral : 15.385 179.460 8659 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.82 % Favored : 88.10 % Rotamer: Outliers : 0.19 % Allowed : 5.71 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.12), residues: 3698 helix: -0.81 (0.12), residues: 1536 sheet: -3.66 (0.22), residues: 349 loop : -3.87 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1544 TYR 0.020 0.002 TYR A 580 PHE 0.025 0.002 PHE A 316 TRP 0.024 0.002 TRP A1582 HIS 0.011 0.002 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (26772) covalent geometry : angle 0.69250 / 0.39 (37716) hydrogen bonds : bond 0.15863 / 11.32 ( 1348) hydrogen bonds : angle 6.86905 / 4.94 ( 3813) Misc. bond : bond 0.14120 / 7.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 26 ASP cc_start: 0.7416 (t70) cc_final: 0.7215 (t70) REVERT: A 108 MET cc_start: 0.2698 (mmp) cc_final: 0.2292 (mmt) REVERT: A 651 TRP cc_start: 0.7959 (m-10) cc_final: 0.7678 (m-10) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.1789 time to fit residues: 106.4898 Evaluate side-chains 218 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 54 HIS A 336 ASN A 601 GLN A1586 HIS ** r 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS N 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.112767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095933 restraints weight = 91833.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.097435 restraints weight = 53133.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098490 restraints weight = 35875.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099082 restraints weight = 26766.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099657 restraints weight = 22153.354| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26774 Z= 0.137 Angle : 0.598 10.765 37716 Z= 0.308 Chirality : 0.043 0.367 4675 Planarity : 0.005 0.080 4463 Dihedral : 15.961 179.125 6251 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.57 % Favored : 90.37 % Rotamer: Outliers : 2.90 % Allowed : 13.44 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.13), residues: 3698 helix: 0.24 (0.13), residues: 1580 sheet: -3.21 (0.22), residues: 367 loop : -3.54 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG r 888 TYR 0.033 0.002 TYR A 256 PHE 0.023 0.002 PHE A 640 TRP 0.036 0.002 TRP I 35 HIS 0.005 0.001 HIS r 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (26772) covalent geometry : angle 0.59839 / 0.31 (37716) hydrogen bonds : bond 0.04506 / 3.11 ( 1348) hydrogen bonds : angle 5.25171 / 3.78 ( 3813) Misc. bond : bond 0.00856 / 0.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3431 (mmp) cc_final: 0.2425 (mmt) REVERT: A 651 TRP cc_start: 0.8283 (m-10) cc_final: 0.7839 (m-10) outliers start: 30 outliers final: 16 residues processed: 249 average time/residue: 0.1477 time to fit residues: 61.6951 Evaluate side-chains 225 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 214 optimal weight: 0.0970 chunk 141 optimal weight: 0.3980 chunk 243 optimal weight: 0.0870 chunk 183 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 chunk 206 optimal weight: 0.0040 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 253 optimal weight: 0.6980 overall best weight: 0.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... r 137 HIS r 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096634 restraints weight = 90859.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098136 restraints weight = 52474.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099195 restraints weight = 35213.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099827 restraints weight = 26388.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.100335 restraints weight = 21665.877| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26774 Z= 0.107 Angle : 0.549 11.349 37716 Z= 0.281 Chirality : 0.041 0.321 4675 Planarity : 0.004 0.070 4463 Dihedral : 15.840 178.219 6251 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.00 % Allowed : 14.80 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 3698 helix: 0.93 (0.13), residues: 1572 sheet: -2.97 (0.23), residues: 361 loop : -3.27 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG r 888 TYR 0.025 0.002 TYR A 208 PHE 0.019 0.001 PHE K 347 TRP 0.046 0.001 TRP I 35 HIS 0.004 0.001 HIS r 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (26772) covalent geometry : angle 0.54932 / 0.28 (37716) hydrogen bonds : bond 0.03997 / 2.75 ( 1348) hydrogen bonds : angle 4.75249 / 3.42 ( 3813) Misc. bond : bond 0.00303 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 28 ARG cc_start: 0.8538 (mmp80) cc_final: 0.7673 (tpm170) REVERT: I 31 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 108 MET cc_start: 0.3360 (mmp) cc_final: 0.2475 (mmt) REVERT: A 150 MET cc_start: 0.7165 (mtp) cc_final: 0.6913 (tpp) REVERT: A 331 TRP cc_start: 0.7069 (OUTLIER) cc_final: 0.6655 (t-100) REVERT: A 651 TRP cc_start: 0.8190 (m-10) cc_final: 0.7866 (m-10) REVERT: A 1591 MET cc_start: 0.7542 (mmt) cc_final: 0.7220 (mmm) REVERT: r 286 ASN cc_start: 0.8442 (m-40) cc_final: 0.8147 (m-40) REVERT: r 433 MET cc_start: 0.6001 (ptm) cc_final: 0.5753 (ptm) outliers start: 31 outliers final: 16 residues processed: 250 average time/residue: 0.1489 time to fit residues: 62.8332 Evaluate side-chains 225 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 76 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 317 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS r 238 ASN r 306 ASN r 903 HIS ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.103660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.085865 restraints weight = 93456.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087213 restraints weight = 55284.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088112 restraints weight = 38140.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088761 restraints weight = 29492.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089102 restraints weight = 24630.615| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 26774 Z= 0.264 Angle : 0.749 14.078 37716 Z= 0.399 Chirality : 0.047 0.267 4675 Planarity : 0.006 0.066 4463 Dihedral : 16.175 176.880 6251 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.41 % Favored : 87.51 % Rotamer: Outliers : 5.80 % Allowed : 13.64 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3698 helix: 0.54 (0.13), residues: 1593 sheet: -2.70 (0.24), residues: 358 loop : -3.27 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 419 TYR 0.034 0.003 TYR A 925 PHE 0.027 0.003 PHE A 582 TRP 0.075 0.003 TRP I 35 HIS 0.018 0.003 HIS r 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (26772) covalent geometry : angle 0.74851 / 0.40 (37716) hydrogen bonds : bond 0.05626 / 3.85 ( 1348) hydrogen bonds : angle 5.14361 / 3.70 ( 3813) Misc. bond : bond 0.00521 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 29 MET cc_start: 0.8310 (ttt) cc_final: 0.7742 (ttt) REVERT: A 108 MET cc_start: 0.5800 (mmp) cc_final: 0.5251 (ptp) REVERT: A 147 MET cc_start: 0.8683 (mmm) cc_final: 0.8481 (mmm) REVERT: A 252 ASP cc_start: 0.6809 (m-30) cc_final: 0.6576 (m-30) REVERT: A 430 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: A 651 TRP cc_start: 0.8708 (m-10) cc_final: 0.8294 (m-10) REVERT: A 1591 MET cc_start: 0.8070 (mmt) cc_final: 0.7750 (mmm) REVERT: r 167 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7810 (t80) REVERT: r 175 GLN cc_start: 0.8394 (tp40) cc_final: 0.8123 (tp40) REVERT: r 323 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7590 (t80) REVERT: q 27 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8818 (tm) outliers start: 60 outliers final: 33 residues processed: 252 average time/residue: 0.1445 time to fit residues: 62.7180 Evaluate side-chains 217 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 165 LEU Chi-restraints excluded: chain r residue 167 TYR Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 253 VAL Chi-restraints excluded: chain r residue 281 ILE Chi-restraints excluded: chain r residue 304 LEU Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 604 LEU Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 64 ASP Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 379 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 192 optimal weight: 0.0000 chunk 341 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 296 optimal weight: 20.0000 chunk 332 optimal weight: 40.0000 chunk 205 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.105897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087805 restraints weight = 91824.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089293 restraints weight = 52599.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090282 restraints weight = 35430.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090928 restraints weight = 26831.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091243 restraints weight = 22319.299| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26774 Z= 0.140 Angle : 0.592 16.047 37716 Z= 0.307 Chirality : 0.042 0.295 4675 Planarity : 0.004 0.069 4463 Dihedral : 16.082 179.800 6251 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.64 % Allowed : 16.44 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3698 helix: 1.20 (0.14), residues: 1580 sheet: -2.51 (0.25), residues: 356 loop : -3.14 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG r 853 TYR 0.036 0.002 TYR A 925 PHE 0.018 0.001 PHE K 347 TRP 0.022 0.002 TRP A1263 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (26772) covalent geometry : angle 0.59191 / 0.31 (37716) hydrogen bonds : bond 0.04108 / 2.76 ( 1348) hydrogen bonds : angle 4.63916 / 3.34 ( 3813) Misc. bond : bond 0.00298 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.5908 (mmp) cc_final: 0.5300 (ptp) REVERT: A 651 TRP cc_start: 0.8652 (m-10) cc_final: 0.8244 (m-10) REVERT: A 1591 MET cc_start: 0.8018 (mmt) cc_final: 0.7666 (mmt) REVERT: r 286 ASN cc_start: 0.8641 (m-40) cc_final: 0.8371 (m-40) REVERT: r 323 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7836 (t80) REVERT: q 27 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8828 (tm) outliers start: 48 outliers final: 26 residues processed: 243 average time/residue: 0.1465 time to fit residues: 61.2448 Evaluate side-chains 214 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 199 LEU Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 64 ASP Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 59 optimal weight: 0.9990 chunk 250 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 42 optimal weight: 0.0040 chunk 221 optimal weight: 1.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS K 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.087406 restraints weight = 91882.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088863 restraints weight = 52826.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089842 restraints weight = 35585.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090367 restraints weight = 27047.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090910 restraints weight = 22864.295| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26774 Z= 0.144 Angle : 0.581 14.229 37716 Z= 0.301 Chirality : 0.042 0.287 4675 Planarity : 0.004 0.063 4463 Dihedral : 16.021 179.809 6251 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 5.13 % Allowed : 16.92 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3698 helix: 1.44 (0.14), residues: 1577 sheet: -2.40 (0.25), residues: 362 loop : -3.06 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 358 TYR 0.035 0.002 TYR A 925 PHE 0.018 0.002 PHE A 473 TRP 0.022 0.001 TRP A1263 HIS 0.008 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (26772) covalent geometry : angle 0.58137 / 0.30 (37716) hydrogen bonds : bond 0.03977 / 2.66 ( 1348) hydrogen bonds : angle 4.48951 / 3.23 ( 3813) Misc. bond : bond 0.00228 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: I 169 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: A 108 MET cc_start: 0.6132 (mmp) cc_final: 0.5325 (ptp) REVERT: A 651 TRP cc_start: 0.8702 (m-10) cc_final: 0.8291 (m-10) REVERT: A 1591 MET cc_start: 0.8044 (mmt) cc_final: 0.7656 (mmt) REVERT: r 286 ASN cc_start: 0.8624 (m-40) cc_final: 0.8336 (m-40) REVERT: r 323 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7829 (t80) REVERT: r 418 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9023 (tt) REVERT: q 27 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (tm) outliers start: 53 outliers final: 34 residues processed: 246 average time/residue: 0.1470 time to fit residues: 61.9096 Evaluate side-chains 227 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 169 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 418 LEU Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 64 ASP Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 48 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 363 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 210 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 238 ASN r 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.101699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083692 restraints weight = 93628.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084956 restraints weight = 55438.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085877 restraints weight = 38502.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086465 restraints weight = 29860.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086891 restraints weight = 25106.649| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 26774 Z= 0.236 Angle : 0.686 13.479 37716 Z= 0.361 Chirality : 0.045 0.270 4675 Planarity : 0.005 0.085 4463 Dihedral : 16.224 178.999 6251 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.41 % Favored : 87.56 % Rotamer: Outliers : 6.19 % Allowed : 16.73 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3698 helix: 1.00 (0.13), residues: 1590 sheet: -2.44 (0.25), residues: 362 loop : -3.18 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 358 TYR 0.028 0.003 TYR A 208 PHE 0.024 0.002 PHE A 279 TRP 0.028 0.002 TRP r 904 HIS 0.012 0.002 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (26772) covalent geometry : angle 0.68602 / 0.36 (37716) hydrogen bonds : bond 0.04927 / 3.33 ( 1348) hydrogen bonds : angle 4.84188 / 3.48 ( 3813) Misc. bond : bond 0.00254 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 187 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 169 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: A 235 MET cc_start: 0.8721 (mmt) cc_final: 0.8517 (mmt) REVERT: A 430 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: r 175 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7741 (tm-30) REVERT: r 286 ASN cc_start: 0.8640 (m-40) cc_final: 0.8377 (m-40) REVERT: r 323 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7783 (t80) REVERT: q 27 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8827 (tm) REVERT: K 378 MET cc_start: 0.4907 (mmp) cc_final: 0.4519 (mmp) outliers start: 64 outliers final: 42 residues processed: 235 average time/residue: 0.1401 time to fit residues: 57.3986 Evaluate side-chains 223 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 169 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 199 LEU Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 419 VAL Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 143 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 367 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 296 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082670 restraints weight = 93540.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.083934 restraints weight = 55346.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084821 restraints weight = 38389.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085360 restraints weight = 29857.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085786 restraints weight = 25295.632| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 26774 Z= 0.257 Angle : 0.693 13.826 37716 Z= 0.366 Chirality : 0.046 0.268 4675 Planarity : 0.005 0.080 4463 Dihedral : 16.309 179.251 6251 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.01 % Favored : 86.88 % Rotamer: Outliers : 6.19 % Allowed : 16.92 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3698 helix: 0.91 (0.13), residues: 1592 sheet: -2.39 (0.25), residues: 362 loop : -3.17 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 358 TYR 0.040 0.003 TYR A 208 PHE 0.027 0.002 PHE A 629 TRP 0.029 0.002 TRP r 904 HIS 0.009 0.002 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 (26772) covalent geometry : angle 0.69336 / 0.37 (37716) hydrogen bonds : bond 0.04933 / 3.32 ( 1348) hydrogen bonds : angle 4.90499 / 3.52 ( 3813) Misc. bond : bond 0.00267 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: I 169 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: A 430 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: r 228 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7805 (m-10) REVERT: r 286 ASN cc_start: 0.8668 (m-40) cc_final: 0.8418 (m-40) REVERT: r 323 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (t80) REVERT: q 27 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8807 (tm) REVERT: K 373 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7873 (mm) REVERT: K 378 MET cc_start: 0.4671 (mmp) cc_final: 0.4263 (mmp) outliers start: 64 outliers final: 45 residues processed: 231 average time/residue: 0.1427 time to fit residues: 57.0662 Evaluate side-chains 229 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 169 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 199 LEU Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 228 PHE Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 419 VAL Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 604 LEU Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 332 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 545 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.103505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085501 restraints weight = 92401.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086809 restraints weight = 53979.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087745 restraints weight = 37180.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088332 restraints weight = 28794.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088785 restraints weight = 24218.106| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26774 Z= 0.122 Angle : 0.588 14.409 37716 Z= 0.304 Chirality : 0.042 0.281 4675 Planarity : 0.004 0.069 4463 Dihedral : 16.183 179.364 6251 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.74 % Allowed : 18.47 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3698 helix: 1.49 (0.14), residues: 1575 sheet: -2.18 (0.26), residues: 357 loop : -2.95 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG r 853 TYR 0.033 0.002 TYR A 454 PHE 0.019 0.001 PHE A 264 TRP 0.025 0.002 TRP A1263 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (26772) covalent geometry : angle 0.58802 / 0.30 (37716) hydrogen bonds : bond 0.03927 / 2.63 ( 1348) hydrogen bonds : angle 4.49705 / 3.23 ( 3813) Misc. bond : bond 0.00226 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: Q 23 ASP cc_start: 0.7586 (t70) cc_final: 0.7355 (t70) REVERT: A 430 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: A 1307 MET cc_start: 0.8125 (mtp) cc_final: 0.7918 (mtp) REVERT: r 175 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7838 (tm-30) REVERT: r 286 ASN cc_start: 0.8569 (m-40) cc_final: 0.8300 (m-40) REVERT: r 323 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7767 (t80) REVERT: q 27 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8801 (tm) REVERT: K 378 MET cc_start: 0.4895 (mmp) cc_final: 0.4492 (mmp) outliers start: 49 outliers final: 30 residues processed: 233 average time/residue: 0.1462 time to fit residues: 58.3772 Evaluate side-chains 219 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 576 ILE Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 301 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082269 restraints weight = 93697.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083531 restraints weight = 55331.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084356 restraints weight = 38495.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084977 restraints weight = 30083.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085269 restraints weight = 25336.562| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 26774 Z= 0.241 Angle : 0.680 14.049 37716 Z= 0.358 Chirality : 0.045 0.269 4675 Planarity : 0.005 0.086 4463 Dihedral : 16.291 179.890 6251 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.41 % Favored : 86.48 % Rotamer: Outliers : 4.26 % Allowed : 18.86 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3698 helix: 1.07 (0.13), residues: 1589 sheet: -2.10 (0.27), residues: 345 loop : -3.08 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 635 TYR 0.028 0.002 TYR A 925 PHE 0.037 0.002 PHE A 629 TRP 0.026 0.002 TRP r 904 HIS 0.007 0.002 HIS r 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (26772) covalent geometry : angle 0.68008 / 0.36 (37716) hydrogen bonds : bond 0.04901 / 3.31 ( 1348) hydrogen bonds : angle 4.80895 / 3.45 ( 3813) Misc. bond : bond 0.00163 / 0.08 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 430 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: r 175 GLN cc_start: 0.8338 (tp-100) cc_final: 0.7933 (tm-30) REVERT: r 286 ASN cc_start: 0.8635 (m-40) cc_final: 0.8373 (m-40) REVERT: r 323 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7766 (t80) REVERT: q 27 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8820 (tm) REVERT: K 373 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7847 (mm) REVERT: K 378 MET cc_start: 0.4501 (mmp) cc_final: 0.4065 (mmp) outliers start: 44 outliers final: 35 residues processed: 220 average time/residue: 0.1449 time to fit residues: 55.3170 Evaluate side-chains 221 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 419 VAL Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 156 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 258 optimal weight: 0.0020 chunk 146 optimal weight: 0.6980 chunk 152 optimal weight: 0.0980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1096 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.104115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086126 restraints weight = 91523.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087461 restraints weight = 53556.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088301 restraints weight = 36916.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088951 restraints weight = 28685.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089425 restraints weight = 24075.242| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26774 Z= 0.113 Angle : 0.583 14.497 37716 Z= 0.299 Chirality : 0.042 0.285 4675 Planarity : 0.004 0.070 4463 Dihedral : 16.137 178.823 6251 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.58 % Allowed : 19.83 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3698 helix: 1.60 (0.14), residues: 1587 sheet: -1.89 (0.27), residues: 346 loop : -2.86 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 358 TYR 0.030 0.002 TYR A 925 PHE 0.021 0.002 PHE A 629 TRP 0.027 0.002 TRP A1263 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26772) covalent geometry : angle 0.58337 / 0.30 (37716) hydrogen bonds : bond 0.03738 / 2.50 ( 1348) hydrogen bonds : angle 4.38304 / 3.15 ( 3813) Misc. bond : bond 0.00199 / 0.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.36 seconds wall clock time: 70 minutes 47.38 seconds (4247.38 seconds total)