Starting phenix.real_space_refine on Tue Aug 26 01:16:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqa_37736/08_2025/8wqa_37736.cif" } resolution = 3.39 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7310 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 182 5.16 5 C 16744 2.51 5 N 4594 2.21 5 O 4953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26479 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 8, 'TRANS': 86} Chain breaks: 1 Chain: "J" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 677 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4930 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12659 SG CYS J 53 50.156 86.190 57.202 1.00 56.35 S ATOM 12682 SG CYS J 56 50.622 83.417 54.506 1.00 66.76 S ATOM 12766 SG CYS J 68 49.019 86.609 53.550 1.00 54.99 S ATOM 12573 SG CYS J 42 51.941 92.902 58.560 1.00 30.52 S ATOM 12592 SG CYS J 45 53.994 89.879 59.735 1.00 30.89 S ATOM 12887 SG CYS J 83 50.304 89.460 59.275 1.00 36.37 S ATOM 12816 SG CYS J 75 46.610 104.746 59.586 1.00 46.47 S ATOM 12983 SG CYS J 94 46.825 102.419 62.065 1.00 42.31 S ATOM 14855 SG CYS I 53 50.174 48.755 156.221 1.00 38.61 S ATOM 14878 SG CYS I 56 48.331 51.601 158.006 1.00 48.27 S ATOM 14962 SG CYS I 68 50.224 48.989 160.043 1.00 48.67 S ATOM 14769 SG CYS I 42 51.950 41.630 153.269 1.00 23.19 S ATOM 14788 SG CYS I 45 53.929 44.894 153.004 1.00 24.22 S ATOM 15080 SG CYS I 83 50.151 45.107 152.961 1.00 27.07 S ATOM 15012 SG CYS I 75 46.885 31.109 153.020 1.00 34.64 S ATOM 15176 SG CYS I 94 47.218 32.837 150.283 1.00 32.67 S Time building chain proxies: 5.41, per 1000 atoms: 0.20 Number of scatterers: 26479 At special positions: 0 Unit cell: (118.08, 136.12, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 182 16.00 O 4953 8.00 N 4594 7.00 C 16744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 910.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 53 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 42 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " Number of angles added : 12 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 16 sheets defined 62.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.686A pdb=" N THR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.829A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 78 removed outlier: 3.516A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.949A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.501A pdb=" N LEU C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 173 removed outlier: 3.673A pdb=" N ILE C 160 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 removed outlier: 3.828A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 228 removed outlier: 3.864A pdb=" N GLN C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 3.793A pdb=" N MET C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.710A pdb=" N TYR C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 260 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.570A pdb=" N ARG C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.908A pdb=" N HIS C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.829A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 357 removed outlier: 4.059A pdb=" N VAL C 340 " --> pdb=" O PRO C 336 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 407 through 423 removed outlier: 3.917A pdb=" N ASP C 413 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.638A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 7.481A pdb=" N TYR C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N GLU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 469 " --> pdb=" O CYS C 465 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 494 removed outlier: 4.024A pdb=" N TYR C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 492 " --> pdb=" O ASN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 548 removed outlier: 4.204A pdb=" N LYS C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 591 removed outlier: 3.885A pdb=" N LEU C 585 " --> pdb=" O GLN C 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE C 588 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.675A pdb=" N THR C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 removed outlier: 4.695A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 661 through 692 removed outlier: 3.663A pdb=" N ARG C 669 " --> pdb=" O MET C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 714 through 728 removed outlier: 3.751A pdb=" N ILE C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 15 removed outlier: 3.708A pdb=" N GLY D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.810A pdb=" N ALA D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.588A pdb=" N ARG D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'D' and resid 123 through 131 removed outlier: 3.634A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.764A pdb=" N ILE D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.964A pdb=" N LYS D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.332A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.527A pdb=" N ASN D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.810A pdb=" N ARG D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.584A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 337 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.140A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 378 Processing helix chain 'D' and resid 381 through 398 Processing helix chain 'D' and resid 403 through 427 Processing helix chain 'D' and resid 432 through 457 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 548 through 562 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 596 through 608 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.937A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 66 through 84 removed outlier: 4.155A pdb=" N LYS E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'F' and resid 23 through 36 removed outlier: 4.070A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.695A pdb=" N GLY F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.732A pdb=" N LYS G 72 " --> pdb=" O HIS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.260A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.596A pdb=" N GLY H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.929A pdb=" N ALA I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 removed outlier: 4.148A pdb=" N THR I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.693A pdb=" N ASN A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.824A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.993A pdb=" N HIS A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.931A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.991A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.752A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 228 removed outlier: 4.144A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.414A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.664A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.595A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.694A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.873A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.593A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 423 removed outlier: 4.005A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.717A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 removed outlier: 7.476A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 494 removed outlier: 4.465A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 547 removed outlier: 4.435A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.883A pdb=" N LEU A 569 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 581 through 591 removed outlier: 3.628A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 removed outlier: 4.146A pdb=" N ASP A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 619 removed outlier: 3.694A pdb=" N LEU A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.564A pdb=" N LYS A 659 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.901A pdb=" N MET A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 removed outlier: 3.878A pdb=" N ILE A 700 " --> pdb=" O HIS A 696 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 3.568A pdb=" N GLU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.801A pdb=" N HIS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.547A pdb=" N CYS B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.790A pdb=" N LYS B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.748A pdb=" N VAL B 170 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.718A pdb=" N PHE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.703A pdb=" N SER B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 262 removed outlier: 3.520A pdb=" N ASN B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.532A pdb=" N GLY B 303 " --> pdb=" O HIS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.562A pdb=" N ILE B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 337 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.931A pdb=" N ILE B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 Processing helix chain 'B' and resid 381 through 398 Processing helix chain 'B' and resid 403 through 426 Processing helix chain 'B' and resid 432 through 457 Processing helix chain 'B' and resid 460 through 478 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.505A pdb=" N THR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 548 through 562 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 596 through 609 Processing helix chain 'B' and resid 617 through 626 removed outlier: 3.599A pdb=" N GLU B 622 " --> pdb=" O ARG B 618 " (cutoff:3.500A) Processing helix chain 'K' and resid -22 through -17 Processing helix chain 'K' and resid -14 through -5 removed outlier: 3.906A pdb=" N ARG K -5 " --> pdb=" O ASN K -9 " (cutoff:3.500A) Processing helix chain 'L' and resid -13 through -3 removed outlier: 4.144A pdb=" N HIS L -4 " --> pdb=" O GLY L -8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 506 through 507 removed outlier: 5.563A pdb=" N SER C 506 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU J 23 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 563 " --> pdb=" O LYS J 25 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP J 27 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 561 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 564 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 575 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 574 " --> pdb=" O PHE C 651 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 510 through 513 removed outlier: 3.601A pdb=" N ALA J 31 " --> pdb=" O TYR C 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'C' and resid 693 through 695 removed outlier: 3.577A pdb=" N LEU C 694 " --> pdb=" O TYR C 741 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.891A pdb=" N GLY D 77 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 86 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.804A pdb=" N LEU E 21 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE E 30 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N ASP F 17 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N LYS E 32 " --> pdb=" O ASP F 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 41 through 42 removed outlier: 3.516A pdb=" N ASN J 47 " --> pdb=" O CYS J 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 31 through 32 removed outlier: 8.016A pdb=" N VAL G 60 " --> pdb=" O TYR G 18 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS G 20 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 18 removed outlier: 7.513A pdb=" N PHE H 4 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL H 75 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET H 6 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU H 77 " --> pdb=" O MET H 6 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG H 8 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE H 79 " --> pdb=" O ARG H 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA H 78 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG H 43 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.529A pdb=" N SER A 506 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU I 23 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 563 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP I 27 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 561 " --> pdb=" O TRP I 27 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 564 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 574 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 510 through 513 Processing sheet with id=AB4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 695 removed outlier: 3.869A pdb=" N LEU A 694 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 742 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 732 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 40 through 42 1365 hydrogen bonds defined for protein. 4029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8780 1.34 - 1.46: 5901 1.46 - 1.58: 12020 1.58 - 1.70: 0 1.70 - 1.82: 284 Bond restraints: 26985 Sorted by residual: bond pdb=" C THR A 654 " pdb=" O THR A 654 " ideal model delta sigma weight residual 1.234 1.263 -0.029 1.55e-02 4.16e+03 3.41e+00 bond pdb=" CG1 ILE D 475 " pdb=" CD1 ILE D 475 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" SD MET A 457 " pdb=" CE MET A 457 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CA ASP A 660 " pdb=" C ASP A 660 " ideal model delta sigma weight residual 1.526 1.513 0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" N THR A 654 " pdb=" CA THR A 654 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.15e-02 7.56e+03 1.37e+00 ... (remaining 26980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 35816 1.98 - 3.96: 531 3.96 - 5.95: 99 5.95 - 7.93: 17 7.93 - 9.91: 10 Bond angle restraints: 36473 Sorted by residual: angle pdb=" N THR A 655 " pdb=" CA THR A 655 " pdb=" C THR A 655 " ideal model delta sigma weight residual 111.36 105.43 5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N THR C 655 " pdb=" CA THR C 655 " pdb=" C THR C 655 " ideal model delta sigma weight residual 111.75 105.79 5.96 1.28e+00 6.10e-01 2.17e+01 angle pdb=" C LYS F 46 " pdb=" N ASP F 47 " pdb=" CA ASP F 47 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA MET A 717 " pdb=" CB MET A 717 " pdb=" CG MET A 717 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA MET E 17 " pdb=" CB MET E 17 " pdb=" CG MET E 17 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 ... (remaining 36468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14613 17.89 - 35.78: 1467 35.78 - 53.68: 273 53.68 - 71.57: 51 71.57 - 89.46: 22 Dihedral angle restraints: 16426 sinusoidal: 6665 harmonic: 9761 Sorted by residual: dihedral pdb=" CA ASN J 76 " pdb=" C ASN J 76 " pdb=" N HIS J 77 " pdb=" CA HIS J 77 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LYS A 621 " pdb=" C LYS A 621 " pdb=" N MET A 622 " pdb=" CA MET A 622 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA MET D 595 " pdb=" C MET D 595 " pdb=" N SER D 596 " pdb=" CA SER D 596 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 16423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2710 0.037 - 0.074: 1071 0.074 - 0.111: 246 0.111 - 0.148: 66 0.148 - 0.184: 12 Chirality restraints: 4105 Sorted by residual: chirality pdb=" CB ILE B 347 " pdb=" CA ILE B 347 " pdb=" CG1 ILE B 347 " pdb=" CG2 ILE B 347 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CG LEU C 559 " pdb=" CB LEU C 559 " pdb=" CD1 LEU C 559 " pdb=" CD2 LEU C 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CB ILE G 90 " pdb=" CA ILE G 90 " pdb=" CG1 ILE G 90 " pdb=" CG2 ILE G 90 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 4102 not shown) Planarity restraints: 4685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 96 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO E 97 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 558 " 0.015 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR C 558 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR C 558 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 558 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C 558 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 558 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 558 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 558 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 94 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO I 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " -0.031 5.00e-02 4.00e+02 ... (remaining 4682 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.20: 24353 3.20 - 3.76: 43509 3.76 - 4.33: 57546 4.33 - 4.90: 94232 Nonbonded interactions: 219932 Sorted by model distance: nonbonded pdb=" CD2 HIS J 77 " pdb="ZN ZN J 202 " model vdw 2.059 1.960 nonbonded pdb=" OD1 ASP D 499 " pdb=" OG1 THR D 503 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR C 219 " pdb=" OE1 GLU C 246 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASN A 624 " pdb=" OG SER A 639 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 167 " pdb=" OD2 ASP B 201 " model vdw 2.223 3.040 ... (remaining 219927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2)))) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 2 through 80 or resid 85 through 100)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 22 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 202)) } ncs_group { reference = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.940 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.003 0.052 27007 Z= 0.147 Angle : 0.641 9.912 36485 Z= 0.346 Chirality : 0.042 0.184 4105 Planarity : 0.004 0.073 4685 Dihedral : 14.891 89.460 10076 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.14 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.70 (0.14), residues: 3269 helix: 0.16 (0.12), residues: 1870 sheet: -0.69 (0.57), residues: 89 loop : -1.27 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 32 TYR 0.040 0.002 TYR C 558 PHE 0.037 0.002 PHE D 392 TRP 0.018 0.001 TRP B 367 HIS 0.006 0.001 HIS J 77 Details of bonding type rmsd covalent geometry : bond 0.00316 (26985) covalent geometry : angle 0.63971 (36473) hydrogen bonds : bond 0.15825 ( 1365) hydrogen bonds : angle 6.28619 ( 4029) metal coordination : bond 0.01213 ( 22) metal coordination : angle 2.56413 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 309 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8876 (tpp) cc_final: 0.7937 (tpt) REVERT: C 538 GLN cc_start: 0.8100 (tp40) cc_final: 0.7419 (pp30) REVERT: A 605 MET cc_start: 0.6007 (pmm) cc_final: 0.5493 (pmm) REVERT: K -3 LEU cc_start: 0.7321 (pp) cc_final: 0.7037 (mp) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.1606 time to fit residues: 82.3389 Evaluate side-chains 260 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0020 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.7508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 508 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.171503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.134796 restraints weight = 44591.815| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.91 r_work: 0.3304 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27007 Z= 0.142 Angle : 0.551 8.707 36485 Z= 0.288 Chirality : 0.040 0.145 4105 Planarity : 0.004 0.056 4685 Dihedral : 4.365 71.688 3585 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.51 % Allowed : 6.97 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.21 (0.15), residues: 3269 helix: 0.58 (0.12), residues: 1950 sheet: -0.88 (0.56), residues: 89 loop : -1.18 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.025 0.001 TYR C 558 PHE 0.025 0.001 PHE D 392 TRP 0.011 0.001 TRP I 87 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00322 (26985) covalent geometry : angle 0.54898 (36473) hydrogen bonds : bond 0.03997 ( 1365) hydrogen bonds : angle 4.59496 ( 4029) metal coordination : bond 0.01065 ( 22) metal coordination : angle 2.56191 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 1.031 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: C 151 MET cc_start: 0.8657 (tpp) cc_final: 0.8191 (tpt) REVERT: C 294 MET cc_start: 0.8273 (mtm) cc_final: 0.7970 (mtm) REVERT: C 447 LEU cc_start: 0.8812 (mm) cc_final: 0.8612 (mt) REVERT: D 70 ARG cc_start: 0.2117 (tpm170) cc_final: 0.1885 (tmt-80) REVERT: D 437 MET cc_start: 0.8425 (tpp) cc_final: 0.7988 (mmt) REVERT: E 18 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7539 (t80) REVERT: A 605 MET cc_start: 0.7171 (pmm) cc_final: 0.5813 (pmm) REVERT: K -3 LEU cc_start: 0.7262 (pp) cc_final: 0.7003 (mp) outliers start: 15 outliers final: 11 residues processed: 299 average time/residue: 0.1408 time to fit residues: 69.3239 Evaluate side-chains 274 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 262 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain H residue 25 PHE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 544 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 147 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 289 optimal weight: 0.2980 chunk 188 optimal weight: 0.6980 chunk 96 optimal weight: 30.0000 chunk 199 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.171026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132823 restraints weight = 44722.845| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 5.08 r_work: 0.3291 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27007 Z= 0.134 Angle : 0.529 9.305 36485 Z= 0.274 Chirality : 0.040 0.202 4105 Planarity : 0.004 0.051 4685 Dihedral : 4.244 71.520 3584 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.00 % Allowed : 9.61 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.07 (0.15), residues: 3269 helix: 0.72 (0.12), residues: 1975 sheet: -1.00 (0.56), residues: 89 loop : -1.21 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.017 0.001 TYR D 163 PHE 0.019 0.001 PHE D 392 TRP 0.010 0.001 TRP I 87 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00304 (26985) covalent geometry : angle 0.52758 (36473) hydrogen bonds : bond 0.03599 ( 1365) hydrogen bonds : angle 4.37665 ( 4029) metal coordination : bond 0.01025 ( 22) metal coordination : angle 2.34405 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 MET cc_start: 0.8547 (ttp) cc_final: 0.8343 (ttm) REVERT: C 151 MET cc_start: 0.8733 (tpp) cc_final: 0.8136 (tpt) REVERT: C 294 MET cc_start: 0.8250 (mtm) cc_final: 0.8039 (mtm) REVERT: C 451 MET cc_start: 0.8003 (mmp) cc_final: 0.7786 (mmp) REVERT: D 70 ARG cc_start: 0.3261 (tpm170) cc_final: 0.2727 (tmt-80) REVERT: E 17 MET cc_start: 0.7549 (tmm) cc_final: 0.7318 (tmm) REVERT: A 566 MET cc_start: 0.6463 (mmp) cc_final: 0.6028 (ptt) REVERT: A 605 MET cc_start: 0.7138 (pmm) cc_final: 0.5826 (pmm) REVERT: K -3 LEU cc_start: 0.7375 (pp) cc_final: 0.7126 (mp) outliers start: 29 outliers final: 22 residues processed: 292 average time/residue: 0.1430 time to fit residues: 68.3100 Evaluate side-chains 286 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 504 ASN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 196 optimal weight: 1.9990 chunk 151 optimal weight: 0.0010 chunk 290 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN C 658 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.169009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131886 restraints weight = 44435.445| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.97 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27007 Z= 0.174 Angle : 0.552 9.838 36485 Z= 0.285 Chirality : 0.041 0.266 4105 Planarity : 0.004 0.051 4685 Dihedral : 4.205 69.371 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.65 % Allowed : 11.33 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.03 (0.15), residues: 3269 helix: 0.77 (0.12), residues: 1968 sheet: -1.20 (0.55), residues: 90 loop : -1.17 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 437 TYR 0.033 0.001 TYR C 558 PHE 0.025 0.001 PHE A 112 TRP 0.008 0.001 TRP I 87 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00411 (26985) covalent geometry : angle 0.54995 (36473) hydrogen bonds : bond 0.03532 ( 1365) hydrogen bonds : angle 4.30624 ( 4029) metal coordination : bond 0.01347 ( 22) metal coordination : angle 2.64758 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8815 (tpp) cc_final: 0.8140 (tpt) REVERT: C 297 MET cc_start: 0.7368 (mmm) cc_final: 0.7128 (mmm) REVERT: C 451 MET cc_start: 0.7945 (mmp) cc_final: 0.7703 (mmp) REVERT: C 538 GLN cc_start: 0.7756 (tp40) cc_final: 0.7371 (pp30) REVERT: A 605 MET cc_start: 0.6396 (pmm) cc_final: 0.5471 (pmm) REVERT: K -17 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (mm) outliers start: 48 outliers final: 29 residues processed: 298 average time/residue: 0.1464 time to fit residues: 72.1676 Evaluate side-chains 287 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 257 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 166 optimal weight: 0.0970 chunk 323 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.169771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133193 restraints weight = 45211.784| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.97 r_work: 0.3270 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27007 Z= 0.149 Angle : 0.542 11.969 36485 Z= 0.279 Chirality : 0.040 0.196 4105 Planarity : 0.004 0.050 4685 Dihedral : 4.178 70.397 3584 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 12.32 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.03 (0.15), residues: 3269 helix: 0.83 (0.12), residues: 1966 sheet: -1.27 (0.55), residues: 90 loop : -1.18 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 437 TYR 0.032 0.001 TYR D 472 PHE 0.020 0.001 PHE D 193 TRP 0.008 0.001 TRP I 87 HIS 0.008 0.001 HIS D 476 Details of bonding type rmsd covalent geometry : bond 0.00350 (26985) covalent geometry : angle 0.54065 (36473) hydrogen bonds : bond 0.03393 ( 1365) hydrogen bonds : angle 4.23714 ( 4029) metal coordination : bond 0.01151 ( 22) metal coordination : angle 2.38979 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 1.094 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: C 151 MET cc_start: 0.8691 (tpp) cc_final: 0.8120 (tpt) REVERT: C 451 MET cc_start: 0.8105 (mmp) cc_final: 0.7895 (mmp) REVERT: C 538 GLN cc_start: 0.8176 (tp40) cc_final: 0.7436 (pp30) REVERT: F 52 ASP cc_start: 0.6428 (p0) cc_final: 0.6198 (p0) REVERT: A 236 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7645 (mpp) REVERT: A 605 MET cc_start: 0.7411 (pmm) cc_final: 0.6060 (pmm) REVERT: A 706 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6255 (mm-40) REVERT: K -17 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7807 (mm) outliers start: 49 outliers final: 34 residues processed: 298 average time/residue: 0.1599 time to fit residues: 78.7214 Evaluate side-chains 294 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 168 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 146 optimal weight: 0.1980 chunk 212 optimal weight: 0.0980 chunk 238 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 281 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.171482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135097 restraints weight = 44459.535| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.82 r_work: 0.3317 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27007 Z= 0.105 Angle : 0.519 11.425 36485 Z= 0.266 Chirality : 0.039 0.208 4105 Planarity : 0.003 0.051 4685 Dihedral : 4.099 73.679 3584 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.65 % Allowed : 12.60 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.17 (0.15), residues: 3269 helix: 0.94 (0.12), residues: 1990 sheet: -1.18 (0.52), residues: 99 loop : -1.13 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 437 TYR 0.019 0.001 TYR D 472 PHE 0.017 0.001 PHE B 626 TRP 0.009 0.001 TRP I 33 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00231 (26985) covalent geometry : angle 0.51829 (36473) hydrogen bonds : bond 0.03156 ( 1365) hydrogen bonds : angle 4.12982 ( 4029) metal coordination : bond 0.00776 ( 22) metal coordination : angle 1.84435 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8622 (tpp) cc_final: 0.8152 (tpt) REVERT: C 534 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6267 (mt-10) REVERT: C 538 GLN cc_start: 0.8185 (tp40) cc_final: 0.7498 (pp30) REVERT: G 17 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6839 (ttm) REVERT: H 19 LYS cc_start: 0.6417 (tptt) cc_final: 0.6117 (tppt) REVERT: A 236 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: A 547 HIS cc_start: 0.7009 (t70) cc_final: 0.6748 (t70) REVERT: A 605 MET cc_start: 0.7529 (pmm) cc_final: 0.6250 (pmm) REVERT: A 706 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.6228 (mm-40) REVERT: K -17 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7693 (mm) REVERT: K -3 LEU cc_start: 0.8131 (mm) cc_final: 0.7801 (pp) outliers start: 48 outliers final: 32 residues processed: 308 average time/residue: 0.1369 time to fit residues: 69.6205 Evaluate side-chains 300 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 55 optimal weight: 10.0000 chunk 307 optimal weight: 0.1980 chunk 314 optimal weight: 0.0040 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.0020 chunk 258 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.171534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134980 restraints weight = 44510.225| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.78 r_work: 0.3334 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27007 Z= 0.106 Angle : 0.519 11.805 36485 Z= 0.265 Chirality : 0.039 0.250 4105 Planarity : 0.003 0.050 4685 Dihedral : 4.060 72.268 3584 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.79 % Allowed : 13.18 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.26 (0.15), residues: 3269 helix: 1.01 (0.12), residues: 1986 sheet: -1.19 (0.52), residues: 99 loop : -1.10 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L -5 TYR 0.022 0.001 TYR B 139 PHE 0.031 0.001 PHE A 112 TRP 0.008 0.001 TRP I 33 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00236 (26985) covalent geometry : angle 0.51801 (36473) hydrogen bonds : bond 0.03086 ( 1365) hydrogen bonds : angle 4.07811 ( 4029) metal coordination : bond 0.00800 ( 22) metal coordination : angle 1.84133 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8684 (tpp) cc_final: 0.8193 (tpt) REVERT: G 17 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6873 (ttm) REVERT: A 236 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7272 (mpp) REVERT: A 547 HIS cc_start: 0.7103 (t70) cc_final: 0.6823 (t70) REVERT: A 605 MET cc_start: 0.7459 (pmm) cc_final: 0.6193 (pmm) REVERT: A 677 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8229 (tptt) REVERT: A 706 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6329 (mm-40) REVERT: B 1 MET cc_start: 0.3624 (ppp) cc_final: 0.3416 (ppp) REVERT: B 193 PHE cc_start: 0.9011 (m-10) cc_final: 0.8782 (m-80) REVERT: K -17 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7637 (mm) REVERT: K -3 LEU cc_start: 0.8097 (mm) cc_final: 0.7852 (pp) outliers start: 52 outliers final: 36 residues processed: 302 average time/residue: 0.1664 time to fit residues: 82.8665 Evaluate side-chains 305 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 224 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 310 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 228 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN A 681 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.170514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.133832 restraints weight = 44578.171| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.91 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27007 Z= 0.132 Angle : 0.542 13.669 36485 Z= 0.275 Chirality : 0.039 0.210 4105 Planarity : 0.003 0.049 4685 Dihedral : 4.045 69.474 3584 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.72 % Allowed : 13.73 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.24 (0.15), residues: 3269 helix: 1.00 (0.12), residues: 1990 sheet: -1.21 (0.51), residues: 99 loop : -1.11 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L -5 TYR 0.019 0.001 TYR D 472 PHE 0.033 0.001 PHE D 392 TRP 0.008 0.001 TRP B 93 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00310 (26985) covalent geometry : angle 0.54063 (36473) hydrogen bonds : bond 0.03119 ( 1365) hydrogen bonds : angle 4.08569 ( 4029) metal coordination : bond 0.01003 ( 22) metal coordination : angle 2.03556 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8765 (tpp) cc_final: 0.8162 (tpt) REVERT: C 236 MET cc_start: 0.7612 (mtt) cc_final: 0.7331 (mtt) REVERT: C 538 GLN cc_start: 0.7821 (tp40) cc_final: 0.7410 (pp30) REVERT: G 17 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6722 (ttm) REVERT: A 236 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7170 (mpp) REVERT: A 605 MET cc_start: 0.6481 (pmm) cc_final: 0.5768 (pmm) REVERT: A 706 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6613 (mm-40) REVERT: B 1 MET cc_start: 0.4053 (ppp) cc_final: 0.3623 (ppp) REVERT: K -17 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7343 (mm) outliers start: 50 outliers final: 36 residues processed: 295 average time/residue: 0.1519 time to fit residues: 74.3056 Evaluate side-chains 298 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 232 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 287 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.171068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.134578 restraints weight = 44541.201| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.77 r_work: 0.3317 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27007 Z= 0.115 Angle : 0.549 12.346 36485 Z= 0.278 Chirality : 0.039 0.313 4105 Planarity : 0.003 0.050 4685 Dihedral : 4.036 69.495 3584 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.72 % Allowed : 13.87 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.26 (0.15), residues: 3269 helix: 1.02 (0.12), residues: 1992 sheet: -1.21 (0.51), residues: 99 loop : -1.13 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L -5 TYR 0.024 0.001 TYR B 139 PHE 0.024 0.001 PHE D 392 TRP 0.008 0.001 TRP I 33 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00262 (26985) covalent geometry : angle 0.54813 (36473) hydrogen bonds : bond 0.03106 ( 1365) hydrogen bonds : angle 4.07557 ( 4029) metal coordination : bond 0.00826 ( 22) metal coordination : angle 1.87300 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8647 (tpp) cc_final: 0.8197 (tpt) REVERT: C 205 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 538 GLN cc_start: 0.8195 (tp40) cc_final: 0.7425 (pp30) REVERT: G 17 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6802 (ttm) REVERT: A 236 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: A 605 MET cc_start: 0.7461 (pmm) cc_final: 0.6175 (pmm) REVERT: A 677 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8338 (mmtp) REVERT: A 706 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.6307 (mm-40) REVERT: B 1 MET cc_start: 0.3818 (ppp) cc_final: 0.3551 (ppp) REVERT: K -17 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7666 (mm) REVERT: K -3 LEU cc_start: 0.7123 (pp) cc_final: 0.6542 (mp) outliers start: 50 outliers final: 39 residues processed: 290 average time/residue: 0.1561 time to fit residues: 74.6401 Evaluate side-chains 300 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 309 optimal weight: 0.0170 chunk 245 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 263 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 270 optimal weight: 40.0000 chunk 119 optimal weight: 0.9980 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K -4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.167563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128606 restraints weight = 44870.714| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 5.48 r_work: 0.3208 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27007 Z= 0.231 Angle : 0.632 11.863 36485 Z= 0.321 Chirality : 0.043 0.332 4105 Planarity : 0.004 0.050 4685 Dihedral : 4.195 64.515 3584 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.79 % Allowed : 13.80 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.03 (0.15), residues: 3269 helix: 0.86 (0.12), residues: 1963 sheet: -1.55 (0.54), residues: 90 loop : -1.21 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 437 TYR 0.024 0.002 TYR C 477 PHE 0.028 0.002 PHE B 626 TRP 0.012 0.001 TRP A 147 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00554 (26985) covalent geometry : angle 0.62989 (36473) hydrogen bonds : bond 0.03521 ( 1365) hydrogen bonds : angle 4.25241 ( 4029) metal coordination : bond 0.01877 ( 22) metal coordination : angle 3.06538 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8855 (tpp) cc_final: 0.8371 (tpt) REVERT: C 297 MET cc_start: 0.8595 (mmm) cc_final: 0.8273 (mmm) REVERT: C 538 GLN cc_start: 0.8281 (tp40) cc_final: 0.7419 (pp30) REVERT: C 581 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: G 17 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6899 (ttm) REVERT: I 86 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7579 (ttt-90) REVERT: A 236 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8533 (mpp) REVERT: A 605 MET cc_start: 0.7370 (pmm) cc_final: 0.5908 (pmm) REVERT: K -17 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7803 (mm) REVERT: K -3 LEU cc_start: 0.7305 (pp) cc_final: 0.6827 (mp) outliers start: 52 outliers final: 37 residues processed: 300 average time/residue: 0.1440 time to fit residues: 71.1649 Evaluate side-chains 301 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 581 GLN Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 627 HIS Chi-restraints excluded: chain K residue -17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 256 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 322 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 0.0970 chunk 251 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 319 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN E 108 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN K -21 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.169450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.132406 restraints weight = 44208.456| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.83 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27007 Z= 0.135 Angle : 0.582 11.780 36485 Z= 0.294 Chirality : 0.040 0.322 4105 Planarity : 0.004 0.050 4685 Dihedral : 4.175 70.248 3584 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.48 % Allowed : 14.25 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.12 (0.15), residues: 3269 helix: 0.94 (0.12), residues: 1971 sheet: -1.44 (0.54), residues: 90 loop : -1.19 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L -5 TYR 0.021 0.001 TYR C 580 PHE 0.023 0.001 PHE D 392 TRP 0.008 0.001 TRP I 33 HIS 0.005 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00315 (26985) covalent geometry : angle 0.58077 (36473) hydrogen bonds : bond 0.03267 ( 1365) hydrogen bonds : angle 4.18391 ( 4029) metal coordination : bond 0.00967 ( 22) metal coordination : angle 2.18564 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.94 seconds wall clock time: 90 minutes 24.16 seconds (5424.16 seconds total)