Starting phenix.real_space_refine on Mon Jul 6 16:56:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd4_31534/07_2026/7fd4_31534.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 136 5.16 5 B 6 2.79 5 C 23460 2.51 5 N 6514 2.21 5 O 7050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37182 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.53, per 1000 atoms: 0.20 Number of scatterers: 37182 At special positions: 0 Unit cell: (182.86, 189.42, 201.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 16 15.00 O 7050 8.00 N 6514 7.00 C 23460 6.00 B 6 5.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 45 sheets defined 47.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.545A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.778A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 185 through 238 Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 259 through 274 removed outlier: 3.943A pdb=" N LYS B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.903A pdb=" N ALA B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.505A pdb=" N GLN B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.521A pdb=" N LYS B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.928A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.867A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.561A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 513 removed outlier: 3.794A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 removed outlier: 3.599A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 561 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.866A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.518A pdb=" N GLU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.707A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 742 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 746 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.790A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 4.701A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 134 removed outlier: 4.752A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.888A pdb=" N LYS C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER C 141 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 removed outlier: 4.378A pdb=" N GLY C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.801A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.928A pdb=" N LEU C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 238 removed outlier: 4.007A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 256 removed outlier: 3.513A pdb=" N VAL C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.754A pdb=" N TYR C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.689A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.790A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.690A pdb=" N GLU C 389 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.594A pdb=" N LYS C 426 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 423 through 427' Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.098A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 removed outlier: 3.809A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 540 through 561 removed outlier: 3.603A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.811A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.522A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.514A pdb=" N LYS C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 660' Processing helix chain 'C' and resid 679 through 692 removed outlier: 3.509A pdb=" N SER C 692 " --> pdb=" O ALA C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.661A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.688A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 746 " --> pdb=" O LEU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.570A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 754 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.792A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 removed outlier: 3.580A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.526A pdb=" N ASN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 182 removed outlier: 4.304A pdb=" N LEU D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 238 removed outlier: 3.742A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.543A pdb=" N MET D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.607A pdb=" N THR D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.751A pdb=" N LYS D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.793A pdb=" N GLU D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.752A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 440 removed outlier: 4.144A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.689A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.982A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 561 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.528A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.575A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.711A pdb=" N LYS D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 729 removed outlier: 3.666A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.677A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.772A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 removed outlier: 3.568A pdb=" N MET E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 139 removed outlier: 3.722A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 185 through 238 Processing helix chain 'E' and resid 247 through 254 removed outlier: 3.917A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 removed outlier: 3.525A pdb=" N ASP E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 removed outlier: 4.244A pdb=" N ALA E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.734A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 339 removed outlier: 3.570A pdb=" N TYR E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 436 through 444 removed outlier: 3.512A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 451 removed outlier: 3.755A pdb=" N THR E 450 " --> pdb=" O GLN E 447 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 451 " --> pdb=" O ASN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 485 removed outlier: 4.052A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 515 removed outlier: 3.904A pdb=" N LYS E 509 " --> pdb=" O TYR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.529A pdb=" N ILE E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 561 Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 647 through 652 removed outlier: 4.005A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 652 " --> pdb=" O THR E 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 647 through 652' Processing helix chain 'E' and resid 679 through 693 removed outlier: 3.657A pdb=" N MET E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.640A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 746 removed outlier: 4.651A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 746 " --> pdb=" O LEU E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 761 through 770 removed outlier: 3.885A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 768 " --> pdb=" O GLU E 764 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 removed outlier: 4.162A pdb=" N ARG F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 139 removed outlier: 3.842A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.610A pdb=" N HIS F 168 " --> pdb=" O THR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.109A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 238 removed outlier: 3.664A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 254 removed outlier: 4.007A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 267 Processing helix chain 'F' and resid 283 through 296 removed outlier: 3.748A pdb=" N ARG F 287 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.552A pdb=" N THR F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 Processing helix chain 'F' and resid 386 through 390 Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.526A pdb=" N HIS F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 427 removed outlier: 3.615A pdb=" N LYS F 426 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET F 427 " --> pdb=" O ILE F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 423 through 427' Processing helix chain 'F' and resid 435 through 444 Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 494 through 513 removed outlier: 3.561A pdb=" N GLN F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Proline residue: F 508 - end of helix Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.521A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 559 removed outlier: 3.704A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 579 removed outlier: 3.594A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 727 removed outlier: 3.742A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 745 removed outlier: 4.987A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 761 through 770 removed outlier: 3.965A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 117 through 136 removed outlier: 4.553A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.895A pdb=" N LYS A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.907A pdb=" N GLN A 148 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.661A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 237 removed outlier: 3.703A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.696A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.575A pdb=" N GLU A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.545A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.780A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 4.212A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 removed outlier: 4.500A pdb=" N ARG A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.614A pdb=" N LYS A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.743A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.934A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 4.244A pdb=" N THR A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.656A pdb=" N ASP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 4.977A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.613A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.868A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.518A pdb=" N MET A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.522A pdb=" N ALA A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 4.788A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.954A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 46 Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.431A pdb=" N LEU B 351 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA B 471 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.804A pdb=" N GLU B 521 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 596 through 602 removed outlier: 5.887A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.840A pdb=" N ALA B 701 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 removed outlier: 4.081A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 91 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 76 removed outlier: 4.176A pdb=" N MET C 75 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 83 " --> pdb=" O MET C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.871A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AB5, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.534A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.987A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 700 through 702 Processing sheet with id=AB8, first strand: chain 'C' and resid 705 through 706 removed outlier: 3.619A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.641A pdb=" N VAL D 7 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 43 through 46 removed outlier: 3.795A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG D 76 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU D 82 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 376 through 380 removed outlier: 3.555A pdb=" N THR D 470 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 350 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 488 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 451 through 452 Processing sheet with id=AC4, first strand: chain 'D' and resid 521 through 522 removed outlier: 6.940A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 622 through 626 removed outlier: 6.264A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N MET D 702 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN D 598 " --> pdb=" O MET D 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 705 through 706 Processing sheet with id=AC7, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.969A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.786A pdb=" N VAL E 86 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 69 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'E' and resid 376 through 378 removed outlier: 6.355A pdb=" N HIS E 377 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.897A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 596 through 600 removed outlier: 6.651A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.446A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 705 through 706 Processing sheet with id=AD6, first strand: chain 'F' and resid 7 through 8 removed outlier: 3.709A pdb=" N VAL F 67 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL F 25 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 7 through 8 removed outlier: 3.709A pdb=" N VAL F 67 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 376 through 380 removed outlier: 6.164A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA F 471 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 520 through 522 removed outlier: 7.011A pdb=" N GLU F 521 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 596 through 603 removed outlier: 6.521A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 701 through 702 Processing sheet with id=AE3, first strand: chain 'F' and resid 705 through 706 removed outlier: 3.690A pdb=" N GLU F 705 " --> pdb=" O MET F 713 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 21 through 25 removed outlier: 6.836A pdb=" N GLN A 83 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 74 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET A 85 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN A 68 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG A 91 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY A 66 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU A 4 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 45 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 47 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 8 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 3 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 104 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 98 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 96 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 21 through 25 Processing sheet with id=AE6, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.549A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 350 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE A 488 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.807A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 596 through 603 removed outlier: 6.544A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.881A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1602 hydrogen bonds defined for protein. 4650 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: 6.62 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 7397 1.32 - 1.48: 13750 1.48 - 1.64: 16456 1.64 - 1.79: 185 1.79 - 1.95: 83 Bond restraints: 37871 Sorted by residual: bond pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.21e-02 6.83e+03 7.76e+01 bond pdb=" C ALA F 679 " pdb=" N GLY F 680 " ideal model delta sigma weight residual 1.331 1.438 -0.108 1.46e-02 4.69e+03 5.47e+01 bond pdb=" N PRO C 677 " pdb=" CA PRO C 677 " ideal model delta sigma weight residual 1.474 1.425 0.049 7.40e-03 1.83e+04 4.38e+01 bond pdb=" C ARG A 432 " pdb=" O ARG A 432 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.22e-02 6.72e+03 2.96e+01 bond pdb=" C PRO B 677 " pdb=" O PRO B 677 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.33e-02 5.65e+03 2.61e+01 ... (remaining 37866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.45: 51255 7.45 - 14.90: 103 14.90 - 22.36: 10 22.36 - 29.81: 1 29.81 - 37.26: 2 Bond angle restraints: 51371 Sorted by residual: angle pdb=" O ALA D 679 " pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 122.42 85.16 37.26 1.61e+00 3.86e-01 5.36e+02 angle pdb=" CA ALA D 679 " pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 118.27 154.06 -35.79 1.59e+00 3.96e-01 5.07e+02 angle pdb=" C ALA D 679 " pdb=" N GLY D 680 " pdb=" CA GLY D 680 " ideal model delta sigma weight residual 120.00 143.91 -23.91 1.10e+00 8.26e-01 4.73e+02 angle pdb=" O ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLY A 680 " ideal model delta sigma weight residual 122.20 102.98 19.22 1.28e+00 6.10e-01 2.26e+02 angle pdb=" O ALA C 679 " pdb=" C ALA C 679 " pdb=" N GLY C 680 " ideal model delta sigma weight residual 122.19 103.48 18.71 1.29e+00 6.01e-01 2.10e+02 ... (remaining 51366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 23053 32.82 - 65.65: 259 65.65 - 98.47: 52 98.47 - 131.30: 7 131.30 - 164.12: 2 Dihedral angle restraints: 23373 sinusoidal: 9814 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.81 -71.19 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ASP B 51 " pdb=" C ASP B 51 " pdb=" N PRO B 52 " pdb=" CA PRO B 52 " ideal model delta harmonic sigma weight residual -180.00 -108.94 -71.06 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -112.95 -67.05 0 5.00e+00 4.00e-02 1.80e+02 ... (remaining 23370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5523 0.126 - 0.251: 300 0.251 - 0.377: 18 0.377 - 0.503: 2 0.503 - 0.629: 1 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CA ASP E 434 " pdb=" N ASP E 434 " pdb=" C ASP E 434 " pdb=" CB ASP E 434 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" CA LEU C 243 " pdb=" N LEU C 243 " pdb=" C LEU C 243 " pdb=" CB LEU C 243 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA LEU F 246 " pdb=" N LEU F 246 " pdb=" C LEU F 246 " pdb=" CB LEU F 246 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 5841 not shown) Planarity restraints: 6657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 4KZ B 802 " -0.206 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C18 4KZ B 802 " 0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ B 802 " -0.263 2.00e-02 2.50e+03 pdb=" N20 4KZ B 802 " 0.340 2.00e-02 2.50e+03 pdb=" O19 4KZ B 802 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ F 802 " 0.200 2.00e-02 2.50e+03 2.15e-01 5.77e+02 pdb=" C18 4KZ F 802 " -0.127 2.00e-02 2.50e+03 pdb=" C21 4KZ F 802 " 0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ F 802 " -0.330 2.00e-02 2.50e+03 pdb=" O19 4KZ F 802 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ E 802 " -0.155 2.00e-02 2.50e+03 1.66e-01 3.43e+02 pdb=" C18 4KZ E 802 " 0.102 2.00e-02 2.50e+03 pdb=" C21 4KZ E 802 " -0.196 2.00e-02 2.50e+03 pdb=" N20 4KZ E 802 " 0.254 2.00e-02 2.50e+03 pdb=" O19 4KZ E 802 " -0.004 2.00e-02 2.50e+03 ... (remaining 6654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4617 2.75 - 3.29: 33524 3.29 - 3.82: 58625 3.82 - 4.36: 69308 4.36 - 4.90: 119821 Nonbonded interactions: 285895 Sorted by model distance: nonbonded pdb=" O GLY F 676 " pdb=" CA PRO F 677 " model vdw 2.212 2.776 nonbonded pdb=" O ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.229 3.040 nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 801 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU D 36 " pdb=" OH TYR D 102 " model vdw 2.246 3.040 nonbonded pdb=" O1B AGS C 801 " pdb=" O2G AGS C 801 " model vdw 2.246 3.040 ... (remaining 285890 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' and (resid 2 through 780 or resid 802)) selection = (chain 'B' and (resid 2 through 780 or resid 802)) selection = (chain 'C' and (resid 2 through 780 or resid 802)) selection = (chain 'D' and (resid 2 through 780 or resid 802)) selection = (chain 'E' and (resid 2 through 780 or resid 802)) selection = (chain 'F' and (resid 2 through 780 or resid 802)) } 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=0.00 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 0.900 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 29.980 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 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 : 0.010 0.137 37877 Z= 0.455 Angle : 1.187 37.259 51371 Z= 0.663 Chirality : 0.066 0.629 5844 Planarity : 0.010 0.222 6657 Dihedral : 11.534 164.121 14641 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 0.41 % Allowed : 2.72 % Favored : 96.87 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 3.26 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.10), residues: 4662 helix: -2.35 (0.09), residues: 2009 sheet: -1.25 (0.19), residues: 639 loop : -2.91 (0.11), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 328 TYR 0.039 0.003 TYR B 97 PHE 0.030 0.003 PHE C 467 TRP 0.043 0.004 TRP F 171 HIS 0.021 0.003 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.45 (37871) covalent geometry : angle 1.18718 / 0.66 (51371) hydrogen bonds : bond 0.16905 / 11.29 ( 1592) hydrogen bonds : angle 6.98852 / 4.89 ( 4650) Misc. bond : bond 0.01407 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 381 time to evaluate : 1.158 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: B 748 LYS cc_start: 0.8988 (mmpt) cc_final: 0.8746 (mppt) REVERT: C 38 MET cc_start: 0.0145 (mmt) cc_final: -0.0237 (mmt) REVERT: C 308 ILE cc_start: 0.8307 (pt) cc_final: 0.8010 (mt) REVERT: C 385 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7646 (ttp-170) REVERT: D 401 MET cc_start: 0.8720 (ptt) cc_final: 0.8461 (ptp) REVERT: E 38 MET cc_start: 0.2035 (mtt) cc_final: 0.1261 (tmm) REVERT: E 75 MET cc_start: 0.1492 (ttp) cc_final: 0.1102 (ttp) REVERT: E 252 LYS cc_start: 0.6662 (ptmt) cc_final: 0.6319 (tttp) REVERT: F 38 MET cc_start: 0.0830 (mtp) cc_final: 0.0593 (ptp) REVERT: F 347 LYS cc_start: 0.7599 (tptt) cc_final: 0.7266 (tmtt) REVERT: F 372 MET cc_start: 0.8660 (mtm) cc_final: 0.8149 (mtm) REVERT: F 390 ILE cc_start: 0.7379 (mm) cc_final: 0.7071 (mp) REVERT: F 393 HIS cc_start: 0.6732 (m-70) cc_final: 0.6413 (m170) REVERT: F 442 VAL cc_start: 0.8187 (p) cc_final: 0.7959 (m) REVERT: F 481 LEU cc_start: 0.8030 (mp) cc_final: 0.7748 (mt) REVERT: F 485 MET cc_start: 0.7022 (pmt) cc_final: 0.5861 (mmm) REVERT: A 323 LYS cc_start: 0.8278 (mmpt) cc_final: 0.7967 (mtpp) REVERT: A 412 VAL cc_start: 0.8005 (t) cc_final: 0.7787 (m) REVERT: A 660 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8521 (mmmt) outliers start: 16 outliers final: 5 residues processed: 395 average time/residue: 0.8726 time to fit residues: 398.1491 Evaluate side-chains 234 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 50.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 HIS B 346 ASN B 495 ASN B 666 HIS C 83 GLN C 138 ASN C 393 HIS C 454 HIS C 664 HIS C 739 ASN C 742 GLN D 12 ASN D 139 HIS D 407 HIS D 510 GLN D 739 ASN E 93 GLN E 138 ASN E 319 HIS E 340 GLN E 510 GLN E 598 GLN E 649 GLN F 49 GLN F 168 HIS F 177 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS A 234 GLN A 319 HIS ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 739 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.177105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102946 restraints weight = 65583.883| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.70 r_work: 0.2990 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37877 Z= 0.160 Angle : 0.677 11.213 51371 Z= 0.343 Chirality : 0.045 0.185 5844 Planarity : 0.006 0.077 6657 Dihedral : 9.620 162.566 5373 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 1.76 % Allowed : 6.82 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.11), residues: 4662 helix: -0.38 (0.11), residues: 2062 sheet: -0.93 (0.19), residues: 651 loop : -2.43 (0.12), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 479 TYR 0.017 0.001 TYR E 289 PHE 0.018 0.002 PHE B 466 TRP 0.018 0.002 TRP F 171 HIS 0.007 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (37871) covalent geometry : angle 0.67729 / 0.34 (51371) hydrogen bonds : bond 0.05152 / 3.49 ( 1592) hydrogen bonds : angle 4.88971 / 3.41 ( 4650) Misc. bond : bond 0.00172 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 1.067 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: symmetry clash REVERT: B 38 MET cc_start: 0.1682 (OUTLIER) cc_final: 0.0753 (pmt) REVERT: C 337 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: C 385 ARG cc_start: 0.8301 (ttp-170) cc_final: 0.7809 (ttp-170) REVERT: C 479 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7564 (mpt180) REVERT: C 511 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8475 (p) REVERT: D 556 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7308 (tttp) REVERT: E 38 MET cc_start: 0.1101 (mtt) cc_final: 0.0371 (tmm) REVERT: E 252 LYS cc_start: 0.6581 (ptmt) cc_final: 0.6147 (tttp) REVERT: E 407 HIS cc_start: 0.8547 (t70) cc_final: 0.7988 (m170) REVERT: E 483 ASP cc_start: 0.7387 (t0) cc_final: 0.7059 (m-30) REVERT: E 622 LYS cc_start: 0.8269 (tttt) cc_final: 0.8017 (ttmm) REVERT: F 75 MET cc_start: 0.0146 (pp-130) cc_final: -0.0928 (tpt) REVERT: F 225 TYR cc_start: 0.8632 (t80) cc_final: 0.8429 (t80) REVERT: F 276 MET cc_start: 0.5325 (mtp) cc_final: 0.4403 (mpp) REVERT: F 347 LYS cc_start: 0.7754 (tptt) cc_final: 0.7393 (tmtt) REVERT: F 393 HIS cc_start: 0.6811 (m-70) cc_final: 0.6522 (m170) REVERT: F 485 MET cc_start: 0.7185 (pmt) cc_final: 0.5979 (mmm) REVERT: F 546 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: A 412 VAL cc_start: 0.7684 (t) cc_final: 0.7384 (m) REVERT: A 591 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8425 (mp0) REVERT: A 660 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8580 (mmmt) REVERT: A 711 LYS cc_start: 0.8786 (tttt) cc_final: 0.8554 (ttmm) outliers start: 69 outliers final: 17 residues processed: 302 average time/residue: 0.7216 time to fit residues: 259.8946 Evaluate side-chains 235 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 277 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 235 optimal weight: 0.0970 chunk 259 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 283 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 434 optimal weight: 0.7980 chunk 396 optimal weight: 8.9990 chunk 355 optimal weight: 7.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN D 346 ASN D 647 HIS E 647 HIS F 139 HIS F 337 GLN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.177876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103907 restraints weight = 66164.933| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.76 r_work: 0.2937 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37877 Z= 0.192 Angle : 0.673 10.646 51371 Z= 0.337 Chirality : 0.046 0.235 5844 Planarity : 0.006 0.074 6657 Dihedral : 8.755 161.912 5371 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 1.91 % Allowed : 8.07 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.54 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.12), residues: 4662 helix: 0.41 (0.12), residues: 2076 sheet: -0.60 (0.20), residues: 652 loop : -2.18 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 385 TYR 0.024 0.002 TYR A 332 PHE 0.025 0.002 PHE B 466 TRP 0.017 0.001 TRP E 602 HIS 0.008 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (37871) covalent geometry : angle 0.67341 / 0.34 (51371) hydrogen bonds : bond 0.05091 / 3.48 ( 1592) hydrogen bonds : angle 4.61312 / 3.21 ( 4650) Misc. bond : bond 0.00072 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 0.919 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: B 38 MET cc_start: 0.2010 (mmt) cc_final: 0.1056 (pmm) REVERT: B 251 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8392 (ttpp) REVERT: B 449 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7959 (OUTLIER) REVERT: B 479 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8112 (mpt180) REVERT: C 385 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.7188 (ttt90) REVERT: D 556 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7225 (tttp) REVERT: D 755 GLU cc_start: 0.8350 (tt0) cc_final: 0.8069 (tt0) REVERT: E 38 MET cc_start: 0.0921 (mtt) cc_final: 0.0190 (tmm) REVERT: E 252 LYS cc_start: 0.6390 (ptmt) cc_final: 0.6055 (tttp) REVERT: E 272 ARG cc_start: 0.5444 (ptm160) cc_final: 0.5155 (mtp-110) REVERT: E 407 HIS cc_start: 0.8556 (t70) cc_final: 0.8010 (m170) REVERT: E 483 ASP cc_start: 0.7482 (t0) cc_final: 0.7132 (m-30) REVERT: E 622 LYS cc_start: 0.8298 (tttt) cc_final: 0.8061 (ttmt) REVERT: F 75 MET cc_start: 0.0537 (pp-130) cc_final: -0.0662 (tmm) REVERT: F 211 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8098 (pm20) REVERT: F 276 MET cc_start: 0.5337 (mtp) cc_final: 0.4360 (mpp) REVERT: F 347 LYS cc_start: 0.7788 (tptt) cc_final: 0.7400 (tmtt) REVERT: F 393 HIS cc_start: 0.6751 (m-70) cc_final: 0.6468 (m170) REVERT: F 485 MET cc_start: 0.7328 (pmt) cc_final: 0.6207 (mmm) REVERT: F 546 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: F 713 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: A 247 GLU cc_start: 0.7955 (mp0) cc_final: 0.7731 (mp0) REVERT: A 412 VAL cc_start: 0.7721 (t) cc_final: 0.7517 (m) REVERT: A 484 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7225 (mtm-85) REVERT: A 591 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8481 (mp0) REVERT: A 660 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8567 (mmmt) REVERT: A 711 LYS cc_start: 0.8771 (tttt) cc_final: 0.8549 (ttmm) outliers start: 75 outliers final: 25 residues processed: 282 average time/residue: 0.6901 time to fit residues: 231.4561 Evaluate side-chains 246 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 484 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 201 optimal weight: 1.9990 chunk 240 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 435 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 229 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 HIS A 168 HIS ** A 454 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 = 0.4362 r_free = 0.4362 target = 0.178871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106990 restraints weight = 66106.827| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.77 r_work: 0.2958 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37877 Z= 0.140 Angle : 0.599 14.213 51371 Z= 0.298 Chirality : 0.044 0.296 5844 Planarity : 0.005 0.070 6657 Dihedral : 8.102 162.285 5369 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.16 % Allowed : 8.80 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.54 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.12), residues: 4662 helix: 0.96 (0.12), residues: 2067 sheet: -0.48 (0.20), residues: 663 loop : -1.97 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 394 TYR 0.020 0.001 TYR A 332 PHE 0.015 0.001 PHE E 466 TRP 0.013 0.001 TRP F 171 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (37871) covalent geometry : angle 0.59933 / 0.30 (51371) hydrogen bonds : bond 0.04112 / 2.79 ( 1592) hydrogen bonds : angle 4.27555 / 2.98 ( 4650) Misc. bond : bond 0.00041 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 227 time to evaluate : 1.294 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8354 (ttpt) REVERT: B 449 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (OUTLIER) REVERT: C 308 ILE cc_start: 0.8031 (pt) cc_final: 0.7590 (mt) REVERT: C 359 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7544 (m) REVERT: C 385 ARG cc_start: 0.8261 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: C 398 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7789 (mm) REVERT: C 479 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8077 (mmp-170) REVERT: C 586 ASP cc_start: 0.8440 (p0) cc_final: 0.8111 (p0) REVERT: C 683 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: D 556 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7163 (tttp) REVERT: D 755 GLU cc_start: 0.8179 (tt0) cc_final: 0.7903 (tt0) REVERT: E 38 MET cc_start: 0.1021 (mtt) cc_final: 0.0453 (tmm) REVERT: E 252 LYS cc_start: 0.6351 (ptmt) cc_final: 0.5952 (tttp) REVERT: E 272 ARG cc_start: 0.5476 (ptm160) cc_final: 0.5173 (mtp-110) REVERT: E 483 ASP cc_start: 0.7450 (t0) cc_final: 0.7112 (m-30) REVERT: E 622 LYS cc_start: 0.8126 (tttt) cc_final: 0.7896 (ttmt) REVERT: F 75 MET cc_start: 0.0492 (pp-130) cc_final: -0.0339 (tmm) REVERT: F 276 MET cc_start: 0.5225 (mtp) cc_final: 0.4416 (mpp) REVERT: F 347 LYS cc_start: 0.7645 (tptt) cc_final: 0.7249 (tmtt) REVERT: F 393 HIS cc_start: 0.6730 (m-70) cc_final: 0.6461 (m170) REVERT: F 485 MET cc_start: 0.7169 (pmt) cc_final: 0.6231 (mmm) REVERT: F 546 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: A 230 MET cc_start: 0.6431 (ptt) cc_final: 0.6163 (pp-130) REVERT: A 234 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: A 247 GLU cc_start: 0.8026 (mp0) cc_final: 0.7768 (mp0) REVERT: A 412 VAL cc_start: 0.7552 (t) cc_final: 0.7348 (m) REVERT: A 484 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: A 591 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8220 (pm20) REVERT: A 660 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8413 (mmmt) REVERT: A 711 LYS cc_start: 0.8645 (tttt) cc_final: 0.8443 (ttmm) REVERT: A 761 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7836 (m-30) outliers start: 85 outliers final: 27 residues processed: 291 average time/residue: 0.7398 time to fit residues: 256.7538 Evaluate side-chains 246 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 466 PHE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 761 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 245 optimal weight: 40.0000 chunk 430 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 436 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 393 optimal weight: 50.0000 chunk 229 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 346 ASN E 454 HIS ** A 454 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 = 0.4352 r_free = 0.4352 target = 0.178219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105211 restraints weight = 65937.830| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.69 r_work: 0.2957 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37877 Z= 0.170 Angle : 0.625 14.568 51371 Z= 0.308 Chirality : 0.045 0.175 5844 Planarity : 0.005 0.071 6657 Dihedral : 7.872 160.935 5369 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 2.01 % Allowed : 9.75 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4662 helix: 1.13 (0.12), residues: 2077 sheet: -0.35 (0.20), residues: 659 loop : -1.89 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 328 TYR 0.021 0.001 TYR A 332 PHE 0.021 0.002 PHE E 466 TRP 0.012 0.001 TRP F 171 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (37871) covalent geometry : angle 0.62493 / 0.31 (51371) hydrogen bonds : bond 0.04320 / 2.94 ( 1592) hydrogen bonds : angle 4.27969 / 2.97 ( 4650) Misc. bond : bond 0.00048 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 213 time to evaluate : 1.452 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: B 251 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8441 (ttpt) REVERT: B 277 GLN cc_start: 0.8709 (tt0) cc_final: 0.8359 (tp40) REVERT: B 449 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8085 (OUTLIER) REVERT: C 308 ILE cc_start: 0.8186 (pt) cc_final: 0.7776 (mt) REVERT: C 359 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7560 (m) REVERT: C 385 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7835 (ttp-170) REVERT: C 479 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7565 (mpt180) REVERT: C 586 ASP cc_start: 0.8442 (p0) cc_final: 0.8155 (p0) REVERT: C 683 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8468 (mtt) REVERT: D 405 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8446 (mm) REVERT: D 556 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7287 (tttp) REVERT: D 748 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8252 (mmmt) REVERT: D 755 GLU cc_start: 0.8280 (tt0) cc_final: 0.8024 (tt0) REVERT: E 38 MET cc_start: 0.0838 (mtt) cc_final: 0.0078 (tmm) REVERT: E 252 LYS cc_start: 0.6339 (ptmt) cc_final: 0.5822 (tttp) REVERT: E 272 ARG cc_start: 0.5536 (ptm160) cc_final: 0.5255 (mtp-110) REVERT: E 401 MET cc_start: 0.5247 (ppp) cc_final: 0.4995 (ppp) REVERT: E 407 HIS cc_start: 0.8489 (t70) cc_final: 0.7933 (m170) REVERT: E 409 MET cc_start: 0.7466 (tpt) cc_final: 0.7203 (mmm) REVERT: E 483 ASP cc_start: 0.7509 (t0) cc_final: 0.7210 (m-30) REVERT: E 622 LYS cc_start: 0.8307 (tttt) cc_final: 0.8078 (ttmm) REVERT: F 75 MET cc_start: 0.0378 (pp-130) cc_final: -0.0811 (tmm) REVERT: F 276 MET cc_start: 0.5206 (mtp) cc_final: 0.4293 (mpp) REVERT: F 347 LYS cc_start: 0.7636 (tptt) cc_final: 0.7199 (tmtt) REVERT: F 393 HIS cc_start: 0.6814 (m-70) cc_final: 0.6531 (m170) REVERT: F 401 MET cc_start: 0.8049 (tpp) cc_final: 0.7795 (tpt) REVERT: F 482 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7357 (tp) REVERT: F 485 MET cc_start: 0.7535 (pmt) cc_final: 0.6706 (mmm) REVERT: F 546 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: A 230 MET cc_start: 0.6716 (ptt) cc_final: 0.6423 (pp-130) REVERT: A 234 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: A 247 GLU cc_start: 0.8183 (mp0) cc_final: 0.7832 (mp0) REVERT: A 484 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: A 591 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8313 (pm20) REVERT: A 660 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8567 (mmmt) outliers start: 79 outliers final: 33 residues processed: 271 average time/residue: 0.7269 time to fit residues: 235.7648 Evaluate side-chains 252 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 222 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 258 optimal weight: 30.0000 chunk 405 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 393 optimal weight: 50.0000 chunk 281 optimal weight: 0.7980 chunk 345 optimal weight: 10.0000 chunk 369 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 177 GLN ** A 454 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 = 0.4350 r_free = 0.4350 target = 0.176598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103454 restraints weight = 65031.200| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.08 r_work: 0.2935 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37877 Z= 0.164 Angle : 0.614 14.747 51371 Z= 0.302 Chirality : 0.044 0.172 5844 Planarity : 0.005 0.074 6657 Dihedral : 7.696 160.786 5369 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 1.91 % Allowed : 10.25 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4662 helix: 1.29 (0.12), residues: 2083 sheet: -0.25 (0.20), residues: 663 loop : -1.81 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 328 TYR 0.017 0.001 TYR F 577 PHE 0.016 0.001 PHE B 466 TRP 0.012 0.001 TRP C 298 HIS 0.006 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (37871) covalent geometry : angle 0.61393 / 0.30 (51371) hydrogen bonds : bond 0.04158 / 2.82 ( 1592) hydrogen bonds : angle 4.18659 / 2.91 ( 4650) Misc. bond : bond 0.00043 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 211 time to evaluate : 1.326 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: B 251 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8387 (ttpt) REVERT: B 277 GLN cc_start: 0.8688 (tt0) cc_final: 0.8206 (tp40) REVERT: C 308 ILE cc_start: 0.8199 (pt) cc_final: 0.7791 (mt) REVERT: C 385 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7930 (ttp-170) REVERT: C 479 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7540 (mpt180) REVERT: C 586 ASP cc_start: 0.8406 (p0) cc_final: 0.8158 (p0) REVERT: C 683 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8479 (mtt) REVERT: D 748 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8274 (mmmt) REVERT: D 755 GLU cc_start: 0.8276 (tt0) cc_final: 0.8028 (tt0) REVERT: E 38 MET cc_start: 0.0665 (mtt) cc_final: -0.0067 (tmm) REVERT: E 252 LYS cc_start: 0.6250 (ptmt) cc_final: 0.5786 (tttp) REVERT: E 272 ARG cc_start: 0.5319 (ptm160) cc_final: 0.5045 (mtp-110) REVERT: E 401 MET cc_start: 0.5312 (ppp) cc_final: 0.5001 (ppp) REVERT: E 409 MET cc_start: 0.7501 (tpt) cc_final: 0.7240 (mmm) REVERT: E 483 ASP cc_start: 0.7487 (t0) cc_final: 0.7160 (m-30) REVERT: E 622 LYS cc_start: 0.8281 (tttt) cc_final: 0.8043 (ttmm) REVERT: F 53 GLU cc_start: 0.1472 (OUTLIER) cc_final: 0.0402 (mm-30) REVERT: F 276 MET cc_start: 0.5329 (mtp) cc_final: 0.4313 (mpp) REVERT: F 347 LYS cc_start: 0.7546 (tptt) cc_final: 0.7124 (tmtt) REVERT: F 393 HIS cc_start: 0.6871 (m-70) cc_final: 0.6606 (m170) REVERT: F 401 MET cc_start: 0.8081 (tpp) cc_final: 0.7831 (tpp) REVERT: F 482 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.6830 (tp) REVERT: F 485 MET cc_start: 0.7526 (pmt) cc_final: 0.6749 (mmt) REVERT: F 546 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 230 MET cc_start: 0.6680 (ptt) cc_final: 0.6359 (pp-130) REVERT: A 234 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: A 247 GLU cc_start: 0.8173 (mp0) cc_final: 0.7795 (mp0) REVERT: A 255 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7485 (mp0) REVERT: A 484 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7229 (mtm-85) REVERT: A 591 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8326 (pm20) REVERT: A 660 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8530 (mmmt) outliers start: 75 outliers final: 38 residues processed: 269 average time/residue: 0.8062 time to fit residues: 258.6867 Evaluate side-chains 248 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 297 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 389 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 453 optimal weight: 4.9990 chunk 314 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 346 ASN D 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.177545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104584 restraints weight = 65823.050| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.63 r_work: 0.2956 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37877 Z= 0.172 Angle : 0.615 14.818 51371 Z= 0.303 Chirality : 0.045 0.172 5844 Planarity : 0.005 0.073 6657 Dihedral : 7.622 160.122 5369 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 1.86 % Allowed : 10.81 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4662 helix: 1.38 (0.12), residues: 2083 sheet: -0.19 (0.20), residues: 663 loop : -1.76 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 328 TYR 0.017 0.001 TYR F 577 PHE 0.017 0.001 PHE B 466 TRP 0.013 0.001 TRP B 298 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (37871) covalent geometry : angle 0.61499 / 0.30 (51371) hydrogen bonds : bond 0.04204 / 2.85 ( 1592) hydrogen bonds : angle 4.16394 / 2.90 ( 4650) Misc. bond : bond 0.00044 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 1.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 251 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8446 (ttpt) REVERT: C 308 ILE cc_start: 0.8207 (pt) cc_final: 0.7809 (mt) REVERT: C 385 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.7891 (ttp-170) REVERT: C 479 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7570 (mpt180) REVERT: C 586 ASP cc_start: 0.8399 (p0) cc_final: 0.8140 (p0) REVERT: C 683 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: D 556 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7616 (tttp) REVERT: D 755 GLU cc_start: 0.8291 (tt0) cc_final: 0.8040 (tt0) REVERT: E 38 MET cc_start: 0.0626 (mtt) cc_final: -0.0158 (tmm) REVERT: E 252 LYS cc_start: 0.6263 (ptmt) cc_final: 0.5785 (tttp) REVERT: E 272 ARG cc_start: 0.5371 (ptm160) cc_final: 0.5096 (mtp-110) REVERT: E 409 MET cc_start: 0.7467 (tpt) cc_final: 0.7178 (mmm) REVERT: E 483 ASP cc_start: 0.7519 (t0) cc_final: 0.7225 (m-30) REVERT: E 622 LYS cc_start: 0.8311 (tttt) cc_final: 0.8080 (ttmm) REVERT: F 53 GLU cc_start: 0.1658 (OUTLIER) cc_final: 0.0490 (mm-30) REVERT: F 276 MET cc_start: 0.5278 (mtp) cc_final: 0.4275 (mpp) REVERT: F 347 LYS cc_start: 0.7475 (tptt) cc_final: 0.7093 (tmtt) REVERT: F 393 HIS cc_start: 0.6872 (m-70) cc_final: 0.6578 (m170) REVERT: F 482 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6989 (tp) REVERT: F 485 MET cc_start: 0.7657 (pmt) cc_final: 0.6922 (mmm) REVERT: F 546 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 230 MET cc_start: 0.6957 (ptt) cc_final: 0.6551 (pp-130) REVERT: A 234 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: A 247 GLU cc_start: 0.8325 (mp0) cc_final: 0.7962 (mp0) REVERT: A 255 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7466 (mp0) REVERT: A 484 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: A 591 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8327 (pm20) REVERT: A 660 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8554 (mmmt) outliers start: 73 outliers final: 37 residues processed: 266 average time/residue: 0.7843 time to fit residues: 247.9910 Evaluate side-chains 249 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 430 optimal weight: 6.9990 chunk 247 optimal weight: 50.0000 chunk 311 optimal weight: 6.9990 chunk 438 optimal weight: 5.9990 chunk 347 optimal weight: 0.0470 chunk 177 optimal weight: 8.9990 chunk 407 optimal weight: 20.0000 chunk 401 optimal weight: 40.0000 chunk 441 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 156 optimal weight: 50.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 393 HIS A 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104320 restraints weight = 65423.423| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.35 r_work: 0.2917 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 37877 Z= 0.227 Angle : 0.666 14.948 51371 Z= 0.328 Chirality : 0.047 0.182 5844 Planarity : 0.005 0.076 6657 Dihedral : 7.693 159.378 5369 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 2.11 % Allowed : 10.97 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4662 helix: 1.35 (0.12), residues: 2080 sheet: -0.19 (0.20), residues: 673 loop : -1.74 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 385 TYR 0.023 0.001 TYR F 577 PHE 0.021 0.001 PHE B 466 TRP 0.013 0.001 TRP C 298 HIS 0.008 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (37871) covalent geometry : angle 0.66611 / 0.33 (51371) hydrogen bonds : bond 0.04674 / 3.17 ( 1592) hydrogen bonds : angle 4.24732 / 2.96 ( 4650) Misc. bond : bond 0.00047 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 206 time to evaluate : 1.120 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: symmetry clash REVERT: B 38 MET cc_start: 0.2146 (mmt) cc_final: 0.1113 (pmm) REVERT: B 247 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 251 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8447 (ttpt) REVERT: C 308 ILE cc_start: 0.8196 (pt) cc_final: 0.7846 (mt) REVERT: C 385 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7948 (ttp-170) REVERT: C 586 ASP cc_start: 0.8418 (p0) cc_final: 0.8188 (p0) REVERT: C 683 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: D 516 MET cc_start: 0.8534 (mmm) cc_final: 0.8293 (mmt) REVERT: D 755 GLU cc_start: 0.8299 (tt0) cc_final: 0.8051 (tt0) REVERT: E 38 MET cc_start: 0.0769 (mtt) cc_final: -0.0067 (tmm) REVERT: E 252 LYS cc_start: 0.6144 (ptmt) cc_final: 0.5526 (tttm) REVERT: E 272 ARG cc_start: 0.5385 (ptm160) cc_final: 0.5053 (mtm-85) REVERT: E 407 HIS cc_start: 0.8496 (t70) cc_final: 0.7931 (m170) REVERT: E 409 MET cc_start: 0.7505 (tpt) cc_final: 0.6889 (mmm) REVERT: E 460 TYR cc_start: -0.0195 (OUTLIER) cc_final: -0.0495 (t80) REVERT: E 622 LYS cc_start: 0.8328 (tttt) cc_final: 0.8082 (ttmm) REVERT: F 53 GLU cc_start: 0.1718 (OUTLIER) cc_final: 0.0391 (mm-30) REVERT: F 225 TYR cc_start: 0.8530 (t80) cc_final: 0.8124 (t80) REVERT: F 276 MET cc_start: 0.5283 (mtp) cc_final: 0.4321 (mpp) REVERT: F 347 LYS cc_start: 0.7429 (tptt) cc_final: 0.7039 (tmtt) REVERT: F 393 HIS cc_start: 0.6580 (m90) cc_final: 0.6363 (m170) REVERT: F 401 MET cc_start: 0.8085 (tpp) cc_final: 0.7843 (tpt) REVERT: F 482 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7082 (tp) REVERT: F 483 ASP cc_start: 0.8551 (m-30) cc_final: 0.8289 (m-30) REVERT: F 485 MET cc_start: 0.7638 (pmt) cc_final: 0.7041 (mmt) REVERT: F 546 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: A 230 MET cc_start: 0.6982 (ptt) cc_final: 0.6562 (pp-130) REVERT: A 234 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: A 247 GLU cc_start: 0.8394 (mp0) cc_final: 0.7996 (mp0) REVERT: A 308 ILE cc_start: 0.8409 (pt) cc_final: 0.8071 (mt) REVERT: A 484 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7264 (mtm-85) REVERT: A 591 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8355 (pm20) outliers start: 83 outliers final: 48 residues processed: 270 average time/residue: 0.7346 time to fit residues: 236.5553 Evaluate side-chains 254 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 460 TYR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 120 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 347 optimal weight: 0.9980 chunk 421 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.178463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105506 restraints weight = 66062.071| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.82 r_work: 0.2954 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37877 Z= 0.135 Angle : 0.598 14.351 51371 Z= 0.293 Chirality : 0.043 0.174 5844 Planarity : 0.005 0.073 6657 Dihedral : 7.480 159.137 5369 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 1.53 % Allowed : 11.70 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4662 helix: 1.56 (0.12), residues: 2079 sheet: -0.11 (0.20), residues: 673 loop : -1.66 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 328 TYR 0.015 0.001 TYR A 332 PHE 0.016 0.001 PHE E 466 TRP 0.015 0.001 TRP A 298 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (37871) covalent geometry : angle 0.59812 / 0.29 (51371) hydrogen bonds : bond 0.03717 / 2.51 ( 1592) hydrogen bonds : angle 4.03285 / 2.81 ( 4650) Misc. bond : bond 0.00036 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.289 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: B 38 MET cc_start: 0.2185 (mmt) cc_final: 0.1178 (pmm) REVERT: B 160 MET cc_start: 0.3866 (mpp) cc_final: 0.2533 (ptp) REVERT: B 247 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: B 251 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8436 (ttpt) REVERT: B 449 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8203 (OUTLIER) REVERT: C 308 ILE cc_start: 0.8193 (pt) cc_final: 0.7778 (mt) REVERT: C 385 ARG cc_start: 0.8391 (ttp-170) cc_final: 0.7933 (ttp-170) REVERT: C 479 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8180 (mmp-170) REVERT: C 586 ASP cc_start: 0.8418 (p0) cc_final: 0.8176 (p0) REVERT: C 683 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: D 755 GLU cc_start: 0.8274 (tt0) cc_final: 0.8032 (tt0) REVERT: E 38 MET cc_start: 0.0540 (mtt) cc_final: -0.0243 (tmt) REVERT: E 252 LYS cc_start: 0.6097 (ptmt) cc_final: 0.5505 (tttm) REVERT: E 272 ARG cc_start: 0.5343 (ptm160) cc_final: 0.5073 (mtp-110) REVERT: E 394 ARG cc_start: 0.5773 (tpp80) cc_final: 0.4920 (mmm-85) REVERT: E 407 HIS cc_start: 0.8510 (t70) cc_final: 0.7921 (m170) REVERT: E 409 MET cc_start: 0.7516 (tpt) cc_final: 0.6823 (mmm) REVERT: E 460 TYR cc_start: -0.0065 (OUTLIER) cc_final: -0.0343 (t80) REVERT: E 622 LYS cc_start: 0.8271 (tttt) cc_final: 0.8046 (ttmm) REVERT: F 53 GLU cc_start: 0.1688 (OUTLIER) cc_final: 0.0513 (mm-30) REVERT: F 225 TYR cc_start: 0.8438 (t80) cc_final: 0.8177 (t80) REVERT: F 276 MET cc_start: 0.5299 (mtp) cc_final: 0.4351 (mpp) REVERT: F 347 LYS cc_start: 0.7418 (tptt) cc_final: 0.7195 (tptt) REVERT: F 482 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7177 (tp) REVERT: F 483 ASP cc_start: 0.8505 (m-30) cc_final: 0.8240 (m-30) REVERT: F 485 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7066 (mmt) REVERT: F 546 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 234 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: A 247 GLU cc_start: 0.8396 (mp0) cc_final: 0.7985 (mp0) REVERT: A 484 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: A 591 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8339 (pm20) outliers start: 60 outliers final: 35 residues processed: 246 average time/residue: 0.7426 time to fit residues: 218.4904 Evaluate side-chains 241 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 460 TYR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 485 MET Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 330 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 433 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 400 optimal weight: 30.0000 chunk 449 optimal weight: 0.4980 chunk 276 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 157 optimal weight: 50.0000 chunk 354 optimal weight: 8.9990 chunk 316 optimal weight: 50.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 393 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.176799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103263 restraints weight = 65140.089| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.63 r_work: 0.2911 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 37877 Z= 0.266 Angle : 0.696 15.100 51371 Z= 0.342 Chirality : 0.048 0.195 5844 Planarity : 0.006 0.076 6657 Dihedral : 7.641 158.118 5369 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 1.40 % Allowed : 12.14 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4662 helix: 1.37 (0.12), residues: 2086 sheet: -0.11 (0.20), residues: 676 loop : -1.69 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 328 TYR 0.025 0.002 TYR F 577 PHE 0.024 0.002 PHE B 466 TRP 0.015 0.002 TRP B 171 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.27 (37871) covalent geometry : angle 0.69551 / 0.34 (51371) hydrogen bonds : bond 0.04853 / 3.29 ( 1592) hydrogen bonds : angle 4.23796 / 2.95 ( 4650) Misc. bond : bond 0.00039 / 0.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.474 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: B 38 MET cc_start: 0.2361 (mmt) cc_final: 0.1296 (pmm) REVERT: B 160 MET cc_start: 0.3799 (mpp) cc_final: 0.2568 (ptp) REVERT: B 247 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 251 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8456 (ttpt) REVERT: B 449 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8170 (OUTLIER) REVERT: C 308 ILE cc_start: 0.8241 (pt) cc_final: 0.7880 (mt) REVERT: C 385 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.8144 (ttp-170) REVERT: C 586 ASP cc_start: 0.8393 (p0) cc_final: 0.8173 (p0) REVERT: D 755 GLU cc_start: 0.8321 (tt0) cc_final: 0.8072 (tt0) REVERT: E 38 MET cc_start: 0.0736 (mtt) cc_final: -0.0059 (tmt) REVERT: E 252 LYS cc_start: 0.6065 (ptmt) cc_final: 0.5474 (tttm) REVERT: E 272 ARG cc_start: 0.5359 (ptm160) cc_final: 0.5055 (tmt170) REVERT: E 407 HIS cc_start: 0.8537 (t70) cc_final: 0.7967 (m170) REVERT: E 409 MET cc_start: 0.7574 (tpt) cc_final: 0.6950 (mmm) REVERT: E 460 TYR cc_start: 0.0080 (OUTLIER) cc_final: -0.0283 (t80) REVERT: E 622 LYS cc_start: 0.8422 (tttt) cc_final: 0.8197 (ttmt) REVERT: F 53 GLU cc_start: 0.1725 (OUTLIER) cc_final: 0.0465 (mm-30) REVERT: F 160 MET cc_start: 0.2406 (mtt) cc_final: 0.2143 (ptt) REVERT: F 225 TYR cc_start: 0.8432 (t80) cc_final: 0.8179 (t80) REVERT: F 276 MET cc_start: 0.5301 (mtp) cc_final: 0.4241 (mpp) REVERT: F 347 LYS cc_start: 0.7403 (tptt) cc_final: 0.6995 (tmtt) REVERT: F 372 MET cc_start: 0.8321 (ttm) cc_final: 0.8081 (ttt) REVERT: F 482 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7325 (tp) REVERT: F 483 ASP cc_start: 0.8502 (m-30) cc_final: 0.8197 (m-30) REVERT: F 485 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7137 (mmt) REVERT: F 546 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: A 247 GLU cc_start: 0.8447 (mp0) cc_final: 0.7974 (mp0) REVERT: A 308 ILE cc_start: 0.8387 (pt) cc_final: 0.8067 (mt) REVERT: A 484 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7276 (mtm-85) REVERT: A 591 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8409 (pm20) outliers start: 55 outliers final: 37 residues processed: 241 average time/residue: 0.8069 time to fit residues: 231.9777 Evaluate side-chains 241 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 460 TYR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 485 MET Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 198 optimal weight: 1.9990 chunk 401 optimal weight: 40.0000 chunk 176 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.178216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104793 restraints weight = 65042.755| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.05 r_work: 0.2953 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 37877 Z= 0.163 Angle : 0.630 16.027 51371 Z= 0.307 Chirality : 0.045 0.207 5844 Planarity : 0.005 0.074 6657 Dihedral : 7.508 158.198 5369 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.78 % Favored : 95.20 % Rotamer: Outliers : 1.25 % Allowed : 12.24 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4662 helix: 1.52 (0.12), residues: 2085 sheet: -0.07 (0.20), residues: 675 loop : -1.62 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 328 TYR 0.016 0.001 TYR F 577 PHE 0.020 0.001 PHE E 466 TRP 0.015 0.001 TRP A 298 HIS 0.008 0.001 HIS F 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (37871) covalent geometry : angle 0.63002 / 0.31 (51371) hydrogen bonds : bond 0.03960 / 2.67 ( 1592) hydrogen bonds : angle 4.05635 / 2.83 ( 4650) Misc. bond : bond 0.00045 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21503.07 seconds wall clock time: 364 minutes 3.10 seconds (21843.10 seconds total)