Starting phenix.real_space_refine on Sun Sep 13 22:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7abf_11694/09_2026/7abf_11694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abf_11694/09_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_11694/09_2026/7abf_11694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abf_11694/09_2026/7abf_11694.map" model { file = "/net/cci-nas-00/data/ceres_data/7abf_11694/09_2026/7abf_11694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abf_11694/09_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-2.2.1-6174/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: 6.05, 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 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: 2.86 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: 6.63 Time building geometry restraints manager: 2.72 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: 37543 4.00 - 8.00: 158 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=" O5' U 5 27 " pdb=" C5' U 5 27 " pdb=" C4' U 5 27 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+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: 5.540 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: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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= 0.235 Angle : 0.727 19.992 37716 Z= 0.440 Chirality : 0.132 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 0.00374 / 0.20 (26772) covalent geometry : angle 0.72723 / 0.44 (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 : 0.880 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: 0.2291 (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: 0.1722 time to fit residues: 102.8330 Evaluate side-chains 217 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 9.9990 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 ** r 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS N 98 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.112766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095898 restraints weight = 91823.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.097409 restraints weight = 53324.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098408 restraints weight = 35860.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.099146 restraints weight = 27011.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099597 restraints weight = 22077.303| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1626 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= 0.132 Angle : 0.606 10.960 37716 Z= 0.308 Chirality : 0.043 0.354 4675 Planarity : 0.005 0.074 4463 Dihedral : 15.918 178.708 6251 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.68 % Favored : 90.27 % Rotamer: Outliers : 3.00 % Allowed : 13.35 % 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: -2.66 (0.13), residues: 3698 helix: 0.26 (0.13), residues: 1580 sheet: -3.16 (0.22), residues: 365 loop : -3.52 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG r 888 TYR 0.034 0.002 TYR A 256 PHE 0.023 0.002 PHE A 640 TRP 0.031 0.002 TRP I 35 HIS 0.008 0.001 HIS r 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (26772) covalent geometry : angle 0.60571 / 0.31 (37716) hydrogen bonds : bond 0.04580 / 3.17 ( 1348) hydrogen bonds : angle 5.20627 / 3.75 ( 3813) Misc. bond : bond 0.01231 / 0.60 ( 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 263 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3463 (mmp) cc_final: 0.2469 (mmt) REVERT: A 651 TRP cc_start: 0.8288 (m-10) cc_final: 0.7845 (m-10) REVERT: r 140 HIS cc_start: 0.6168 (m170) cc_final: 0.5957 (m170) outliers start: 31 outliers final: 17 residues processed: 251 average time/residue: 0.1501 time to fit residues: 63.3259 Evaluate side-chains 221 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 373 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: 0.9990 chunk 141 optimal weight: 0.0570 chunk 243 optimal weight: 0.0270 chunk 183 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 253 optimal weight: 10.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... r 140 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 = 0.3883 r_free = 0.3883 target = 0.111619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094629 restraints weight = 90774.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096132 restraints weight = 52905.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097118 restraints weight = 35531.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097848 restraints weight = 26832.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098265 restraints weight = 21922.466| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 26774 Z= 0.119 Angle : 0.561 12.068 37716 Z= 0.286 Chirality : 0.042 0.315 4675 Planarity : 0.004 0.064 4463 Dihedral : 15.801 179.061 6251 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.29 % Allowed : 14.12 % Favored : 82.59 % 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: -1.98 (0.14), residues: 3698 helix: 0.98 (0.13), residues: 1567 sheet: -2.91 (0.23), residues: 357 loop : -3.27 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG r 888 TYR 0.024 0.002 TYR A 925 PHE 0.023 0.001 PHE K 347 TRP 0.045 0.002 TRP I 35 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (26772) covalent geometry : angle 0.56140 / 0.29 (37716) hydrogen bonds : bond 0.04090 / 2.82 ( 1348) hydrogen bonds : angle 4.72377 / 3.40 ( 3813) Misc. bond : bond 0.00900 / 0.43 ( 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 258 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7272 (mtp) cc_final: 0.6981 (tpp) REVERT: A 331 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6604 (t-100) REVERT: A 651 TRP cc_start: 0.8273 (m-10) cc_final: 0.7851 (m-10) REVERT: r 607 LEU cc_start: 0.8668 (tm) cc_final: 0.8465 (tp) outliers start: 34 outliers final: 20 residues processed: 247 average time/residue: 0.1443 time to fit residues: 60.3342 Evaluate side-chains 228 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 73 LEU 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 509 HIS Chi-restraints excluded: chain A residue 1095 ILE 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 1295 ILE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 76 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 332 optimal weight: 0.4980 chunk 177 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 137 optimal weight: 0.4980 chunk 317 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.104824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086998 restraints weight = 93642.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088373 restraints weight = 55505.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089256 restraints weight = 38296.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089942 restraints weight = 29581.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090403 restraints weight = 24573.662| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 26774 Z= 0.233 Angle : 0.692 13.077 37716 Z= 0.363 Chirality : 0.046 0.339 4675 Planarity : 0.005 0.062 4463 Dihedral : 15.994 178.620 6251 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.82 % Favored : 88.07 % Rotamer: Outliers : 5.71 % Allowed : 14.12 % Favored : 80.17 % 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: -1.98 (0.14), residues: 3698 helix: 0.88 (0.13), residues: 1582 sheet: -2.73 (0.24), residues: 375 loop : -3.24 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG r 177 TYR 0.039 0.003 TYR A 925 PHE 0.031 0.002 PHE K 347 TRP 0.076 0.003 TRP I 35 HIS 0.018 0.002 HIS A1712 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (26772) covalent geometry : angle 0.69216 / 0.36 (37716) hydrogen bonds : bond 0.04981 / 3.41 ( 1348) hydrogen bonds : angle 4.90325 / 3.52 ( 3813) Misc. bond : bond 0.00620 / 0.31 ( 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 268 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 MET cc_start: 0.8282 (ttt) cc_final: 0.7766 (ttt) REVERT: A 147 MET cc_start: 0.8668 (mmm) cc_final: 0.8391 (mmm) REVERT: A 630 TRP cc_start: 0.7414 (p90) cc_final: 0.7170 (p90) REVERT: A 651 TRP cc_start: 0.8623 (m-10) cc_final: 0.8172 (m-10) REVERT: r 165 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8780 (tp) REVERT: r 172 PHE cc_start: 0.7748 (m-80) cc_final: 0.7463 (m-10) REVERT: q 27 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8836 (tm) outliers start: 59 outliers final: 31 residues processed: 252 average time/residue: 0.1428 time to fit residues: 61.4549 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 : 0.878 ------------------------------------------------------------------------------- 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 114 ILE 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 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 1046 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 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 188 VAL Chi-restraints excluded: chain r residue 189 VAL 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 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 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: 2.9990 chunk 100 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 341 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 296 optimal weight: 20.0000 chunk 332 optimal weight: 40.0000 chunk 205 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 208 HIS r 238 ASN r 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.106523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088741 restraints weight = 91574.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090137 restraints weight = 53730.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091043 restraints weight = 36992.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091738 restraints weight = 28467.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092054 restraints weight = 23687.999| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26774 Z= 0.136 Angle : 0.598 16.779 37716 Z= 0.305 Chirality : 0.042 0.299 4675 Planarity : 0.004 0.065 4463 Dihedral : 15.932 179.971 6251 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.13 % Allowed : 16.34 % Favored : 78.53 % 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: -1.58 (0.14), residues: 3698 helix: 1.33 (0.14), residues: 1573 sheet: -2.52 (0.25), residues: 359 loop : -3.13 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 635 TYR 0.033 0.002 TYR A 925 PHE 0.023 0.001 PHE A 640 TRP 0.067 0.002 TRP I 35 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (26772) covalent geometry : angle 0.59758 / 0.30 (37716) hydrogen bonds : bond 0.04026 / 2.73 ( 1348) hydrogen bonds : angle 4.56269 / 3.28 ( 3813) Misc. bond : bond 0.00203 / 0.10 ( 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 259 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: A 651 TRP cc_start: 0.8592 (m-10) cc_final: 0.8175 (m-10) REVERT: A 1048 MET cc_start: 0.7740 (mmp) cc_final: 0.7471 (mmp) REVERT: A 1591 MET cc_start: 0.8415 (mmm) cc_final: 0.8157 (mmt) REVERT: r 172 PHE cc_start: 0.7721 (m-80) cc_final: 0.7479 (m-10) REVERT: r 286 ASN cc_start: 0.8607 (m-40) cc_final: 0.8297 (m-40) REVERT: r 323 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7580 (t80) REVERT: r 418 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9088 (tt) REVERT: r 607 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8696 (tp) REVERT: q 27 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8752 (tm) outliers start: 53 outliers final: 31 residues processed: 251 average time/residue: 0.1414 time to fit residues: 61.3507 Evaluate side-chains 229 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 114 ILE Chi-restraints excluded: chain I residue 161 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 316 PHE Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 1046 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 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain r residue 137 HIS 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 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 418 LEU Chi-restraints excluded: chain r residue 604 LEU Chi-restraints excluded: chain r residue 607 LEU 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 385 ARG 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: 0.9980 chunk 250 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 221 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS r 238 ASN r 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.107202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089590 restraints weight = 90993.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090990 restraints weight = 53570.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091972 restraints weight = 36607.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092586 restraints weight = 27885.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092988 restraints weight = 23314.831| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26774 Z= 0.118 Angle : 0.567 17.176 37716 Z= 0.288 Chirality : 0.042 0.301 4675 Planarity : 0.004 0.059 4463 Dihedral : 15.842 179.497 6251 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.32 % Allowed : 15.57 % Favored : 79.11 % 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: -1.27 (0.15), residues: 3698 helix: 1.63 (0.14), residues: 1567 sheet: -2.37 (0.25), residues: 359 loop : -3.00 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 358 TYR 0.024 0.002 TYR A 925 PHE 0.021 0.001 PHE A 640 TRP 0.057 0.001 TRP I 35 HIS 0.007 0.001 HIS r 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (26772) covalent geometry : angle 0.56714 / 0.29 (37716) hydrogen bonds : bond 0.03703 / 2.50 ( 1348) hydrogen bonds : angle 4.35810 / 3.13 ( 3813) Misc. bond : bond 0.00178 / 0.09 ( 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 261 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.8832 (mp) cc_final: 0.8513 (mm) REVERT: A 430 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.7494 (m-10) REVERT: A 651 TRP cc_start: 0.8576 (m-10) cc_final: 0.8198 (m-10) REVERT: A 1591 MET cc_start: 0.8455 (mmm) cc_final: 0.8159 (mmt) REVERT: r 172 PHE cc_start: 0.7685 (m-80) cc_final: 0.7450 (m-10) REVERT: r 286 ASN cc_start: 0.8560 (m-40) cc_final: 0.8270 (m-40) REVERT: r 323 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7623 (t80) REVERT: r 607 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8686 (tp) REVERT: q 27 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8713 (tm) outliers start: 55 outliers final: 31 residues processed: 250 average time/residue: 0.1429 time to fit residues: 61.3069 Evaluate side-chains 231 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 114 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 404 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 1046 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 1478 LEU Chi-restraints excluded: chain A residue 1536 LEU 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 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 199 LEU Chi-restraints excluded: chain r residue 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 607 LEU Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 64 ASP Chi-restraints excluded: chain K residue 325 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 48 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 372 optimal weight: 7.9990 chunk 363 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 347 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN ** r 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.106980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089376 restraints weight = 91276.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090783 restraints weight = 53902.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091701 restraints weight = 36721.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092402 restraints weight = 28074.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092848 restraints weight = 23103.141| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26774 Z= 0.117 Angle : 0.563 16.380 37716 Z= 0.284 Chirality : 0.041 0.308 4675 Planarity : 0.004 0.059 4463 Dihedral : 15.805 179.461 6251 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 5.32 % Allowed : 15.47 % Favored : 79.21 % 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: -1.14 (0.15), residues: 3698 helix: 1.73 (0.14), residues: 1570 sheet: -2.24 (0.26), residues: 359 loop : -2.93 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 358 TYR 0.033 0.002 TYR A 925 PHE 0.017 0.001 PHE A 640 TRP 0.014 0.001 TRP A1263 HIS 0.005 0.001 HIS r 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (26772) covalent geometry : angle 0.56341 / 0.28 (37716) hydrogen bonds : bond 0.03618 / 2.44 ( 1348) hydrogen bonds : angle 4.25622 / 3.06 ( 3813) Misc. bond : bond 0.00138 / 0.07 ( 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 260 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 126 ILE cc_start: 0.8817 (mp) cc_final: 0.8589 (mm) REVERT: A 430 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: A 651 TRP cc_start: 0.8633 (m-10) cc_final: 0.8235 (m-10) REVERT: A 1048 MET cc_start: 0.7786 (mmp) cc_final: 0.7527 (mmp) REVERT: A 1591 MET cc_start: 0.8454 (mmm) cc_final: 0.8145 (mmt) REVERT: r 172 PHE cc_start: 0.7674 (m-80) cc_final: 0.7437 (m-10) REVERT: r 286 ASN cc_start: 0.8549 (m-40) cc_final: 0.8291 (m-40) REVERT: r 323 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7568 (t80) REVERT: r 607 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8693 (tp) REVERT: q 27 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (tm) REVERT: K 324 LYS cc_start: 0.7055 (tptt) cc_final: 0.6823 (ptpp) REVERT: K 378 MET cc_start: 0.4899 (mmp) cc_final: 0.4538 (mmp) outliers start: 55 outliers final: 38 residues processed: 245 average time/residue: 0.1414 time to fit residues: 60.2037 Evaluate side-chains 241 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 114 ILE 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 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 509 HIS Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1143 MET 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 1478 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain r residue 137 HIS 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 208 HIS Chi-restraints excluded: chain r residue 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 607 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 55 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 143 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 296 optimal weight: 30.0000 chunk 201 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.099741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.081840 restraints weight = 94689.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083093 restraints weight = 56487.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083985 restraints weight = 39237.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084499 restraints weight = 30554.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084930 restraints weight = 25930.157| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.170 26774 Z= 0.326 Angle : 0.816 15.701 37716 Z= 0.426 Chirality : 0.050 0.364 4675 Planarity : 0.006 0.075 4463 Dihedral : 16.275 178.582 6251 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.14 % Favored : 85.72 % Rotamer: Outliers : 5.80 % Allowed : 16.15 % Favored : 78.05 % 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: -2.10 (0.14), residues: 3698 helix: 0.57 (0.13), residues: 1600 sheet: -2.37 (0.25), residues: 364 loop : -3.23 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 419 TYR 0.040 0.003 TYR A 225 PHE 0.029 0.003 PHE A 279 TRP 0.040 0.003 TRP r 904 HIS 0.014 0.003 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.33 (26772) covalent geometry : angle 0.81576 / 0.43 (37716) hydrogen bonds : bond 0.05965 / 4.08 ( 1348) hydrogen bonds : angle 5.16894 / 3.70 ( 3813) Misc. bond : bond 0.00101 / 0.05 ( 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 245 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: Q 29 MET cc_start: 0.8229 (ttt) cc_final: 0.7803 (ttt) REVERT: A 430 TRP cc_start: 0.8678 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: r 175 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7894 (tm-30) REVERT: r 323 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7771 (t80) REVERT: r 433 MET cc_start: 0.7727 (ppp) cc_final: 0.7464 (ptm) REVERT: q 27 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8828 (tm) REVERT: q 64 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8342 (p0) REVERT: K 324 LYS cc_start: 0.7563 (tptt) cc_final: 0.7270 (ptpp) REVERT: K 373 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7955 (mm) outliers start: 60 outliers final: 42 residues processed: 228 average time/residue: 0.1411 time to fit residues: 56.2774 Evaluate side-chains 223 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 114 ILE 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 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 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1143 MET 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 1478 LEU 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 189 VAL Chi-restraints excluded: chain r residue 199 LEU Chi-restraints excluded: chain r residue 205 THR 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 604 LEU Chi-restraints excluded: chain r residue 607 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 332 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.102622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084724 restraints weight = 92876.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086042 restraints weight = 54676.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086948 restraints weight = 37622.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087585 restraints weight = 29116.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087869 restraints weight = 24312.560| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26774 Z= 0.156 Angle : 0.630 16.703 37716 Z= 0.324 Chirality : 0.044 0.333 4675 Planarity : 0.004 0.065 4463 Dihedral : 16.161 179.765 6251 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.65 % Favored : 89.32 % Rotamer: Outliers : 5.42 % Allowed : 16.73 % Favored : 77.85 % 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: -1.56 (0.14), residues: 3698 helix: 1.18 (0.13), residues: 1588 sheet: -2.28 (0.26), residues: 361 loop : -3.03 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 358 TYR 0.032 0.002 TYR A 925 PHE 0.025 0.002 PHE A1490 TRP 0.027 0.002 TRP r 904 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (26772) covalent geometry : angle 0.63006 / 0.32 (37716) hydrogen bonds : bond 0.04271 / 2.88 ( 1348) hydrogen bonds : angle 4.62876 / 3.33 ( 3813) Misc. bond : bond 0.00171 / 0.09 ( 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 255 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: I 169 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: A 430 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: A 1048 MET cc_start: 0.7884 (mmp) cc_final: 0.7670 (mmp) REVERT: r 175 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7772 (tm-30) REVERT: r 286 ASN cc_start: 0.8559 (m-40) cc_final: 0.8284 (m-40) REVERT: r 323 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7673 (t80) REVERT: r 433 MET cc_start: 0.7542 (ppp) cc_final: 0.7254 (ptm) REVERT: q 1 MET cc_start: 0.7708 (ttt) cc_final: 0.7412 (ttt) REVERT: q 27 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8766 (tm) REVERT: K 324 LYS cc_start: 0.7467 (tptt) cc_final: 0.7170 (ptpp) REVERT: K 378 MET cc_start: 0.4765 (mmp) cc_final: 0.4277 (mmp) outliers start: 56 outliers final: 39 residues processed: 241 average time/residue: 0.1381 time to fit residues: 58.3228 Evaluate side-chains 234 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 114 ILE 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 1046 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 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 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 205 THR 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 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: 0.9980 chunk 141 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 352 optimal weight: 0.0970 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.102201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084122 restraints weight = 92943.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085514 restraints weight = 53719.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086410 restraints weight = 36401.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087095 restraints weight = 27905.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087442 restraints weight = 23189.362| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26774 Z= 0.176 Angle : 0.639 18.305 37716 Z= 0.327 Chirality : 0.044 0.350 4675 Planarity : 0.005 0.069 4463 Dihedral : 16.097 179.833 6251 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 4.06 % Allowed : 18.18 % Favored : 77.76 % 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: -1.38 (0.14), residues: 3698 helix: 1.36 (0.13), residues: 1584 sheet: -2.06 (0.27), residues: 350 loop : -2.99 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 358 TYR 0.027 0.002 TYR A 925 PHE 0.024 0.002 PHE A 629 TRP 0.030 0.002 TRP A1263 HIS 0.005 0.001 HIS r 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (26772) covalent geometry : angle 0.63919 / 0.33 (37716) hydrogen bonds : bond 0.04248 / 2.87 ( 1348) hydrogen bonds : angle 4.55731 / 3.27 ( 3813) Misc. bond : bond 0.00163 / 0.09 ( 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 235 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: I 169 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: A 430 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: r 286 ASN cc_start: 0.8560 (m-40) cc_final: 0.8271 (m-40) REVERT: r 323 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7745 (t80) REVERT: r 433 MET cc_start: 0.7668 (ppp) cc_final: 0.7407 (ptm) REVERT: q 1 MET cc_start: 0.7661 (ttt) cc_final: 0.7380 (ttt) REVERT: q 27 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (tm) REVERT: K 324 LYS cc_start: 0.7594 (tptt) cc_final: 0.7185 (ptpp) REVERT: K 378 MET cc_start: 0.4693 (mmp) cc_final: 0.4177 (mmp) outliers start: 42 outliers final: 33 residues processed: 224 average time/residue: 0.1372 time to fit residues: 53.5634 Evaluate side-chains 226 residues out of total 3359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 114 ILE 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 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 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 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 253 VAL Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 419 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 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 156 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 258 optimal weight: 0.0570 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 HIS r 140 HIS K 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087003 restraints weight = 91528.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088342 restraints weight = 53656.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089233 restraints weight = 36904.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089885 restraints weight = 28572.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090246 restraints weight = 23883.820| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26774 Z= 0.111 Angle : 0.587 17.586 37716 Z= 0.296 Chirality : 0.042 0.323 4675 Planarity : 0.004 0.065 4463 Dihedral : 15.966 179.074 6251 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.48 % Allowed : 19.44 % 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: -1.03 (0.15), residues: 3698 helix: 1.73 (0.14), residues: 1585 sheet: -1.98 (0.26), residues: 360 loop : -2.87 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG r 853 TYR 0.031 0.001 TYR A 925 PHE 0.022 0.001 PHE I 90 TRP 0.027 0.002 TRP A1263 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (26772) covalent geometry : angle 0.58659 / 0.30 (37716) hydrogen bonds : bond 0.03621 / 2.44 ( 1348) hydrogen bonds : angle 4.27671 / 3.08 ( 3813) Misc. bond : bond 0.00184 / 0.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.33 seconds wall clock time: 69 minutes 52.28 seconds (4192.28 seconds total)