Starting phenix.real_space_refine on Thu May 29 15:16:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqa_37736/05_2025/8wqa_37736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqa_37736/05_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_37736/05_2025/8wqa_37736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqa_37736/05_2025/8wqa_37736.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqa_37736/05_2025/8wqa_37736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqa_37736/05_2025/8wqa_37736.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: 15.32, per 1000 atoms: 0.58 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: 7.06 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.37 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: 9.84 Time building geometry restraints manager: 8.26 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 104 or resid 200 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: 12.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.310 Process input model: 68.770 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.370 ------------------------------------------------------------------------------- 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 : 9.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP B 367 HIS 0.006 0.001 HIS J 77 PHE 0.037 0.002 PHE D 392 TYR 0.040 0.002 TYR C 558 ARG 0.011 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.15825 ( 1365) hydrogen bonds : angle 6.28619 ( 4029) metal coordination : bond 0.01213 ( 22) metal coordination : angle 2.56413 ( 12) covalent geometry : bond 0.00316 (26985) covalent geometry : angle 0.63971 (36473) *********************** 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 : 2.736 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: 0.3560 time to fit residues: 181.0799 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 : 2.549 ------------------------------------------------------------------------------- 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 273 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 0.0040 chunk 189 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 241 HIS ** 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 = 0.4331 r_free = 0.4331 target = 0.172089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134223 restraints weight = 44471.536| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.02 r_work: 0.3328 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27007 Z= 0.132 Angle : 0.544 8.715 36485 Z= 0.285 Chirality : 0.040 0.147 4105 Planarity : 0.004 0.056 4685 Dihedral : 4.355 72.157 3585 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.48 % Allowed : 6.73 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3269 helix: 0.61 (0.12), residues: 1947 sheet: -0.85 (0.56), residues: 89 loop : -1.17 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 367 HIS 0.005 0.001 HIS L -4 PHE 0.025 0.001 PHE D 392 TYR 0.026 0.001 TYR C 558 ARG 0.006 0.000 ARG L -5 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 1365) hydrogen bonds : angle 4.57595 ( 4029) metal coordination : bond 0.00922 ( 22) metal coordination : angle 2.47399 ( 12) covalent geometry : bond 0.00295 (26985) covalent geometry : angle 0.54246 (36473) *********************** 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 308 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 294 time to evaluate : 3.173 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: 0.8597 (ttp) cc_final: 0.8385 (ttm) REVERT: C 151 MET cc_start: 0.8677 (tpp) cc_final: 0.8177 (tpt) REVERT: C 294 MET cc_start: 0.8202 (mtm) cc_final: 0.7901 (mtm) REVERT: D 70 ARG cc_start: 0.2841 (tpm170) cc_final: 0.2352 (tmt-80) REVERT: D 437 MET cc_start: 0.8331 (tpp) cc_final: 0.7873 (mmt) REVERT: E 18 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 605 MET cc_start: 0.6943 (pmm) cc_final: 0.5664 (pmm) REVERT: A 606 ASN cc_start: 0.8401 (p0) cc_final: 0.8159 (p0) REVERT: K -3 LEU cc_start: 0.7398 (pp) cc_final: 0.7171 (mp) outliers start: 14 outliers final: 10 residues processed: 302 average time/residue: 0.3455 time to fit residues: 171.1244 Evaluate side-chains 277 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 266 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 544 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 34 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 225 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 504 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.171325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.134661 restraints weight = 44730.100| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 4.08 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27007 Z= 0.137 Angle : 0.531 9.163 36485 Z= 0.274 Chirality : 0.040 0.207 4105 Planarity : 0.004 0.052 4685 Dihedral : 4.223 71.024 3584 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.06 % Allowed : 9.75 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3269 helix: 0.75 (0.12), residues: 1965 sheet: -0.99 (0.56), residues: 89 loop : -1.18 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 87 HIS 0.005 0.001 HIS C 88 PHE 0.020 0.001 PHE B 626 TYR 0.019 0.001 TYR D 163 ARG 0.007 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1365) hydrogen bonds : angle 4.35639 ( 4029) metal coordination : bond 0.01023 ( 22) metal coordination : angle 2.35344 ( 12) covalent geometry : bond 0.00317 (26985) covalent geometry : angle 0.52911 (36473) *********************** 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 316 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 3.092 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: 0.8840 (tpp) cc_final: 0.8122 (tpt) REVERT: C 451 MET cc_start: 0.7928 (mmp) cc_final: 0.7718 (mmp) REVERT: E 17 MET cc_start: 0.7480 (tmm) cc_final: 0.7247 (tmm) REVERT: A 605 MET cc_start: 0.6363 (pmm) cc_final: 0.5377 (pmm) REVERT: A 657 MET cc_start: 0.4355 (OUTLIER) cc_final: 0.4135 (tpt) REVERT: B 193 PHE cc_start: 0.7312 (m-80) cc_final: 0.6967 (m-10) outliers start: 31 outliers final: 21 residues processed: 299 average time/residue: 0.3637 time to fit residues: 177.0479 Evaluate side-chains 292 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 2.930 ------------------------------------------------------------------------------- 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 92 GLU Chi-restraints excluded: chain J residue 36 ASP 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 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 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 657 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 222 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 283 HIS C 538 GLN C 547 HIS C 658 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.165556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120931 restraints weight = 44854.800| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.01 r_work: 0.3345 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27007 Z= 0.311 Angle : 0.672 9.580 36485 Z= 0.347 Chirality : 0.045 0.214 4105 Planarity : 0.004 0.055 4685 Dihedral : 4.414 65.662 3584 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.92 % Allowed : 11.74 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3269 helix: 0.49 (0.12), residues: 1973 sheet: -1.45 (0.54), residues: 90 loop : -1.30 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 27 HIS 0.011 0.001 HIS C 88 PHE 0.031 0.002 PHE B 626 TYR 0.035 0.002 TYR C 558 ARG 0.011 0.001 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 1365) hydrogen bonds : angle 4.52735 ( 4029) metal coordination : bond 0.02632 ( 22) metal coordination : angle 3.74679 ( 12) covalent geometry : bond 0.00742 (26985) covalent geometry : angle 0.66845 (36473) *********************** 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 325 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 3.002 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: 0.8746 (tpp) cc_final: 0.8256 (tpt) REVERT: C 451 MET cc_start: 0.8258 (mmp) cc_final: 0.7962 (mmp) REVERT: F 52 ASP cc_start: 0.6505 (p0) cc_final: 0.6283 (p0) REVERT: A 556 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 605 MET cc_start: 0.7321 (pmm) cc_final: 0.5941 (pmm) REVERT: A 657 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.4221 (tpt) REVERT: K -17 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7972 (mm) outliers start: 56 outliers final: 32 residues processed: 300 average time/residue: 0.3496 time to fit residues: 173.2745 Evaluate side-chains 285 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 THR 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 568 MET 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 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 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 281 LEU 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 81 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 315 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.124717 restraints weight = 44536.365| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.05 r_work: 0.3402 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27007 Z= 0.145 Angle : 0.550 12.281 36485 Z= 0.283 Chirality : 0.040 0.227 4105 Planarity : 0.004 0.053 4685 Dihedral : 4.296 73.804 3584 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.96 % Allowed : 12.80 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3269 helix: 0.69 (0.12), residues: 1987 sheet: -1.50 (0.54), residues: 90 loop : -1.24 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 33 HIS 0.005 0.001 HIS B 565 PHE 0.021 0.001 PHE D 193 TYR 0.037 0.001 TYR D 472 ARG 0.007 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1365) hydrogen bonds : angle 4.31734 ( 4029) metal coordination : bond 0.01116 ( 22) metal coordination : angle 2.48365 ( 12) covalent geometry : bond 0.00337 (26985) covalent geometry : angle 0.54812 (36473) *********************** 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 330 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 3.032 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 151 MET cc_start: 0.8615 (tpp) cc_final: 0.8168 (tpt) REVERT: C 297 MET cc_start: 0.8432 (mmm) cc_final: 0.8054 (mmm) REVERT: C 451 MET cc_start: 0.8168 (mmp) cc_final: 0.7844 (mmp) REVERT: C 534 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6257 (mt-10) REVERT: C 538 GLN cc_start: 0.8200 (tp40) cc_final: 0.7412 (pp30) REVERT: F 52 ASP cc_start: 0.6370 (p0) cc_final: 0.6130 (p0) REVERT: A 236 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8566 (mpp) REVERT: A 556 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7837 (pp) REVERT: A 605 MET cc_start: 0.7435 (pmm) cc_final: 0.6140 (pmm) REVERT: A 657 MET cc_start: 0.4643 (OUTLIER) cc_final: 0.4020 (tpt) REVERT: B 565 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6169 (m-70) REVERT: K -17 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (mm) REVERT: K -3 LEU cc_start: 0.8158 (mm) cc_final: 0.7831 (pp) outliers start: 57 outliers final: 40 residues processed: 306 average time/residue: 0.3761 time to fit residues: 187.2085 Evaluate side-chains 304 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET 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 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 F residue 23 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 53 CYS 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 63 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 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 539 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 211 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.169774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133092 restraints weight = 44551.464| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.86 r_work: 0.3288 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27007 Z= 0.117 Angle : 0.531 11.380 36485 Z= 0.273 Chirality : 0.039 0.206 4105 Planarity : 0.004 0.051 4685 Dihedral : 4.203 76.015 3584 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.20 % Allowed : 12.87 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3269 helix: 0.85 (0.12), residues: 1982 sheet: -1.43 (0.55), residues: 90 loop : -1.16 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 33 HIS 0.004 0.001 HIS B 565 PHE 0.018 0.001 PHE B 626 TYR 0.020 0.001 TYR C 477 ARG 0.006 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 1365) hydrogen bonds : angle 4.19279 ( 4029) metal coordination : bond 0.00881 ( 22) metal coordination : angle 2.07766 ( 12) covalent geometry : bond 0.00265 (26985) covalent geometry : angle 0.52935 (36473) *********************** 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 345 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 281 time to evaluate : 2.844 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: 0.8711 (tpp) cc_final: 0.8230 (tpt) REVERT: C 297 MET cc_start: 0.8617 (mmm) cc_final: 0.8231 (mmm) REVERT: C 451 MET cc_start: 0.8025 (mmp) cc_final: 0.7797 (mmp) REVERT: C 534 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6230 (mt-10) REVERT: C 538 GLN cc_start: 0.8198 (tp40) cc_final: 0.7446 (pp30) REVERT: F 52 ASP cc_start: 0.6455 (p0) cc_final: 0.6252 (p0) REVERT: G 17 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6878 (ttm) REVERT: A 236 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7964 (mpp) REVERT: A 556 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7798 (pp) REVERT: A 605 MET cc_start: 0.7430 (pmm) cc_final: 0.6154 (pmm) REVERT: A 657 MET cc_start: 0.4594 (OUTLIER) cc_final: 0.3923 (tpt) REVERT: B 1 MET cc_start: 0.3600 (ppp) cc_final: 0.3382 (ppp) REVERT: B 193 PHE cc_start: 0.9053 (m-10) cc_final: 0.8820 (m-80) REVERT: B 565 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6303 (m-70) REVERT: K -17 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7835 (mm) REVERT: K -3 LEU cc_start: 0.8110 (mm) cc_final: 0.7891 (pp) outliers start: 64 outliers final: 41 residues processed: 319 average time/residue: 0.3426 time to fit residues: 179.7546 Evaluate side-chains 309 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET 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 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 F residue 41 GLU 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 27 LEU 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 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 65 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 291 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 243 optimal weight: 0.0270 chunk 269 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 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 = 0.4305 r_free = 0.4305 target = 0.169793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.133199 restraints weight = 44546.847| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.88 r_work: 0.3286 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27007 Z= 0.120 Angle : 0.539 13.524 36485 Z= 0.275 Chirality : 0.039 0.208 4105 Planarity : 0.004 0.049 4685 Dihedral : 4.154 74.377 3584 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.92 % Allowed : 13.59 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3269 helix: 0.92 (0.12), residues: 1979 sheet: -1.43 (0.54), residues: 90 loop : -1.15 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 33 HIS 0.004 0.001 HIS C 88 PHE 0.021 0.001 PHE B 130 TYR 0.020 0.001 TYR B 139 ARG 0.007 0.000 ARG L -5 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 1365) hydrogen bonds : angle 4.13388 ( 4029) metal coordination : bond 0.00919 ( 22) metal coordination : angle 2.03838 ( 12) covalent geometry : bond 0.00275 (26985) covalent geometry : angle 0.53779 (36473) *********************** 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: 56 poor density : 270 time to evaluate : 3.096 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 151 MET cc_start: 0.8791 (tpp) cc_final: 0.8295 (tpt) REVERT: C 205 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7882 (mt-10) REVERT: C 297 MET cc_start: 0.8661 (mmm) cc_final: 0.8278 (mmm) REVERT: C 476 MET cc_start: 0.8008 (mtm) cc_final: 0.7737 (mtm) REVERT: G 17 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6905 (ttm) REVERT: A 236 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: A 556 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 566 MET cc_start: 0.6271 (mmp) cc_final: 0.5911 (ptt) REVERT: A 605 MET cc_start: 0.7413 (pmm) cc_final: 0.6119 (pmm) REVERT: A 657 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.3900 (tpt) REVERT: B 1 MET cc_start: 0.3621 (ppp) cc_final: 0.3417 (ppp) REVERT: B 193 PHE cc_start: 0.9061 (m-10) cc_final: 0.8804 (m-80) REVERT: B 565 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6254 (m-70) REVERT: K -17 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7798 (mm) REVERT: K -3 LEU cc_start: 0.8136 (mm) cc_final: 0.7877 (pp) outliers start: 56 outliers final: 43 residues processed: 303 average time/residue: 0.3445 time to fit residues: 171.2570 Evaluate side-chains 312 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 137 MET 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 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 F residue 41 GLU 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 21 LEU 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 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 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 200 optimal weight: 0.4980 chunk 246 optimal weight: 30.0000 chunk 202 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 286 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN C 581 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 = 0.4275 r_free = 0.4275 target = 0.167201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123333 restraints weight = 44794.917| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27007 Z= 0.199 Angle : 0.596 11.243 36485 Z= 0.304 Chirality : 0.042 0.211 4105 Planarity : 0.004 0.050 4685 Dihedral : 4.213 68.085 3584 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.06 % Allowed : 14.07 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3269 helix: 0.83 (0.12), residues: 1974 sheet: -1.61 (0.54), residues: 90 loop : -1.19 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.008 0.001 HIS C 88 PHE 0.026 0.001 PHE B 626 TYR 0.022 0.001 TYR C 477 ARG 0.009 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1365) hydrogen bonds : angle 4.22815 ( 4029) metal coordination : bond 0.01642 ( 22) metal coordination : angle 2.74099 ( 12) covalent geometry : bond 0.00474 (26985) covalent geometry : angle 0.59387 (36473) *********************** 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 334 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 2.758 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 151 MET cc_start: 0.8725 (tpp) cc_final: 0.8253 (tpt) REVERT: C 201 LYS cc_start: 0.9392 (tptp) cc_final: 0.9164 (tptp) REVERT: C 297 MET cc_start: 0.8553 (mmm) cc_final: 0.8205 (mmm) REVERT: C 476 MET cc_start: 0.8012 (mtm) cc_final: 0.7730 (mtm) REVERT: C 581 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7259 (pp30) REVERT: F 52 ASP cc_start: 0.6566 (p0) cc_final: 0.6347 (p0) REVERT: G 17 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6917 (ttm) REVERT: I 88 LEU cc_start: 0.9143 (mm) cc_final: 0.8884 (mm) REVERT: A 236 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8430 (mpp) REVERT: A 556 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 566 MET cc_start: 0.6192 (mmp) cc_final: 0.5977 (ptt) REVERT: A 605 MET cc_start: 0.7362 (pmm) cc_final: 0.6090 (pmm) REVERT: A 657 MET cc_start: 0.4580 (OUTLIER) cc_final: 0.3890 (tpt) REVERT: B 1 MET cc_start: 0.3581 (ppp) cc_final: 0.3379 (ppp) REVERT: B 193 PHE cc_start: 0.9016 (m-10) cc_final: 0.8735 (m-80) REVERT: B 565 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6121 (m-70) REVERT: K -17 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7864 (mm) REVERT: K -3 LEU cc_start: 0.8190 (mm) cc_final: 0.7918 (pp) outliers start: 60 outliers final: 49 residues processed: 311 average time/residue: 0.3383 time to fit residues: 172.3419 Evaluate side-chains 322 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 137 MET 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 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 90 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 F residue 41 GLU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 21 LEU 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 27 LEU Chi-restraints excluded: chain H residue 63 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 237 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 196 optimal weight: 0.5980 chunk 312 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 308 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 258 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** E 108 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.168909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133741 restraints weight = 44602.621| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.95 r_work: 0.3261 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27007 Z= 0.133 Angle : 0.565 11.746 36485 Z= 0.287 Chirality : 0.040 0.219 4105 Planarity : 0.004 0.049 4685 Dihedral : 4.201 72.381 3584 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.99 % Allowed : 14.45 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3269 helix: 0.89 (0.12), residues: 1979 sheet: -1.53 (0.54), residues: 90 loop : -1.19 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 33 HIS 0.005 0.001 HIS H 10 PHE 0.022 0.001 PHE B 130 TYR 0.021 0.001 TYR C 477 ARG 0.008 0.000 ARG L -5 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 1365) hydrogen bonds : angle 4.16725 ( 4029) metal coordination : bond 0.00901 ( 22) metal coordination : angle 2.14099 ( 12) covalent geometry : bond 0.00308 (26985) covalent geometry : angle 0.56410 (36473) *********************** 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 328 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 2.970 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: 0.8664 (tpp) cc_final: 0.8210 (tpt) REVERT: C 297 MET cc_start: 0.8621 (mmm) cc_final: 0.8311 (mmm) REVERT: C 476 MET cc_start: 0.8017 (mtm) cc_final: 0.7724 (mtm) REVERT: C 538 GLN cc_start: 0.8359 (tp40) cc_final: 0.7563 (pp30) REVERT: C 547 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6669 (t70) REVERT: G 17 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6865 (ttm) REVERT: I 88 LEU cc_start: 0.9165 (mm) cc_final: 0.8923 (mm) REVERT: A 42 ILE cc_start: 0.8841 (mt) cc_final: 0.8608 (tt) REVERT: A 236 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8480 (mpp) REVERT: A 556 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (pp) REVERT: A 605 MET cc_start: 0.7473 (pmm) cc_final: 0.6167 (pmm) REVERT: A 657 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3775 (tpt) REVERT: A 723 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: B 1 MET cc_start: 0.3662 (ppp) cc_final: 0.3440 (ppp) REVERT: B 193 PHE cc_start: 0.9014 (m-10) cc_final: 0.8727 (m-80) REVERT: B 462 GLU cc_start: 0.7317 (tp30) cc_final: 0.7075 (tp30) REVERT: B 565 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6078 (m-70) REVERT: K -17 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7844 (mm) REVERT: K -3 LEU cc_start: 0.8238 (mm) cc_final: 0.7978 (pp) outliers start: 58 outliers final: 44 residues processed: 307 average time/residue: 0.3495 time to fit residues: 175.5593 Evaluate side-chains 312 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 137 MET 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 547 HIS 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 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 53 CYS Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 21 LEU 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 27 LEU Chi-restraints excluded: chain H residue 70 GLN 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 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 149 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 242 optimal weight: 0.1980 chunk 213 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** H 10 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** 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 = 0.4301 r_free = 0.4301 target = 0.169405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132831 restraints weight = 44592.610| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.82 r_work: 0.3290 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27007 Z= 0.124 Angle : 0.567 11.644 36485 Z= 0.287 Chirality : 0.040 0.230 4105 Planarity : 0.004 0.049 4685 Dihedral : 4.167 73.367 3584 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.82 % Allowed : 14.73 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3269 helix: 0.97 (0.12), residues: 1966 sheet: -1.49 (0.54), residues: 90 loop : -1.15 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 33 HIS 0.004 0.001 HIS C 88 PHE 0.022 0.001 PHE B 130 TYR 0.034 0.001 TYR B 139 ARG 0.009 0.000 ARG L -5 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 1365) hydrogen bonds : angle 4.13887 ( 4029) metal coordination : bond 0.00881 ( 22) metal coordination : angle 2.01749 ( 12) covalent geometry : bond 0.00287 (26985) covalent geometry : angle 0.56547 (36473) ********************** 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 324 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 2.894 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: 0.8671 (tpp) cc_final: 0.8195 (tpt) REVERT: C 476 MET cc_start: 0.7987 (mtm) cc_final: 0.7664 (mtm) REVERT: C 538 GLN cc_start: 0.8310 (tp40) cc_final: 0.7537 (pp30) REVERT: C 547 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.6623 (t70) REVERT: G 17 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6837 (ttm) REVERT: I 88 LEU cc_start: 0.9124 (mm) cc_final: 0.8868 (mm) REVERT: A 42 ILE cc_start: 0.8833 (mt) cc_final: 0.8604 (tt) REVERT: A 236 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (mpp) REVERT: A 556 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 605 MET cc_start: 0.7435 (pmm) cc_final: 0.6153 (pmm) REVERT: A 657 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.3700 (tpt) REVERT: A 723 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: B 193 PHE cc_start: 0.8940 (m-10) cc_final: 0.8669 (m-80) REVERT: B 384 ASP cc_start: 0.7363 (m-30) cc_final: 0.7045 (m-30) REVERT: B 462 GLU cc_start: 0.7290 (tp30) cc_final: 0.7051 (tp30) REVERT: B 565 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6226 (m-70) REVERT: K -17 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7790 (mm) REVERT: K -3 LEU cc_start: 0.8247 (mm) cc_final: 0.7984 (pp) outliers start: 53 outliers final: 43 residues processed: 303 average time/residue: 0.3606 time to fit residues: 180.1531 Evaluate side-chains 314 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 137 MET 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 547 HIS 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 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 53 CYS Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 21 LEU 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 27 LEU 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 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 565 HIS 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 218 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 D 468 ASN J 76 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** 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 = 0.4289 r_free = 0.4289 target = 0.168700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131172 restraints weight = 44583.655| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.21 r_work: 0.3250 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27007 Z= 0.127 Angle : 0.569 11.510 36485 Z= 0.289 Chirality : 0.040 0.231 4105 Planarity : 0.004 0.048 4685 Dihedral : 4.148 72.341 3584 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.89 % Allowed : 14.80 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3269 helix: 0.99 (0.12), residues: 1966 sheet: -1.49 (0.54), residues: 90 loop : -1.14 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 33 HIS 0.004 0.001 HIS C 88 PHE 0.023 0.001 PHE B 130 TYR 0.019 0.001 TYR B 277 ARG 0.008 0.000 ARG L -5 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 1365) hydrogen bonds : angle 4.11977 ( 4029) metal coordination : bond 0.00915 ( 22) metal coordination : angle 1.99188 ( 12) covalent geometry : bond 0.00295 (26985) covalent geometry : angle 0.56761 (36473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13272.11 seconds wall clock time: 231 minutes 24.62 seconds (13884.62 seconds total)