Starting phenix.real_space_refine on Fri Jun 27 14:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqe_37742/06_2025/8wqe_37742.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7310 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 182 5.16 5 C 16635 2.51 5 N 4557 2.21 5 O 4921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26301 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 8, 'TRANS': 86} Chain breaks: 1 Chain: "J" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "I" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4930 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 91 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12659 SG CYS J 53 50.576 87.401 57.834 1.00 11.17 S ATOM 12682 SG CYS J 56 51.041 85.259 54.827 1.00 19.84 S ATOM 12766 SG CYS J 68 50.471 89.032 54.489 1.00 16.88 S ATOM 12573 SG CYS J 42 52.225 94.691 59.982 1.00 3.89 S ATOM 12592 SG CYS J 45 54.412 91.575 60.631 1.00 4.83 S ATOM 12884 SG CYS J 83 50.702 91.139 60.680 1.00 5.37 S ATOM 12816 SG CYS J 75 46.677 105.659 60.911 1.00 10.80 S ATOM 12980 SG CYS J 94 46.168 102.966 62.918 1.00 8.94 S ATOM 14875 SG CYS I 53 50.009 48.726 156.252 1.00 6.10 S ATOM 14898 SG CYS I 56 48.423 51.589 158.255 1.00 9.88 S ATOM 14982 SG CYS I 68 50.041 48.678 160.080 1.00 10.82 S ATOM 14789 SG CYS I 42 51.909 41.614 153.508 1.00 2.32 S ATOM 14808 SG CYS I 45 53.897 44.869 153.304 1.00 2.92 S ATOM 15100 SG CYS I 83 50.167 45.098 153.275 1.00 3.42 S ATOM 15032 SG CYS I 75 46.744 30.673 153.100 1.00 5.89 S ATOM 15196 SG CYS I 94 47.420 32.655 150.580 1.00 5.79 S Time building chain proxies: 15.39, per 1000 atoms: 0.59 Number of scatterers: 26301 At special positions: 0 Unit cell: (117.26, 137.76, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 182 16.00 O 4921 8.00 N 4557 7.00 C 16635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 53 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 42 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " Number of angles added : 12 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 18 sheets defined 61.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.611A pdb=" N LEU C 17 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.937A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 78 removed outlier: 3.675A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.633A pdb=" N LEU C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 172 removed outlier: 3.679A pdb=" N ILE C 160 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.744A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.785A pdb=" N GLN C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 254 removed outlier: 3.775A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 268 removed outlier: 3.534A pdb=" N VAL C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 290 through 304 removed outlier: 4.240A pdb=" N ALA C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 327 removed outlier: 3.998A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 357 removed outlier: 3.751A pdb=" N VAL C 340 " --> pdb=" O PRO C 336 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 407 through 423 removed outlier: 3.618A pdb=" N VAL C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 415 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.989A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 7.667A pdb=" N TYR C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N GLU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C 469 " --> pdb=" O CYS C 465 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 4.483A pdb=" N ALA C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 547 removed outlier: 4.353A pdb=" N LYS C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 539 " --> pdb=" O LYS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 591 removed outlier: 4.381A pdb=" N ALA C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 584 " --> pdb=" O TYR C 580 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 585 " --> pdb=" O GLN C 581 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 604 removed outlier: 3.599A pdb=" N ASP C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 602 " --> pdb=" O GLU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 removed outlier: 3.562A pdb=" N LEU C 610 " --> pdb=" O ASN C 606 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.556A pdb=" N LYS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 691 Processing helix chain 'C' and resid 695 through 708 Processing helix chain 'C' and resid 714 through 727 Processing helix chain 'D' and resid 2 through 15 removed outlier: 3.891A pdb=" N GLY D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.538A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 123 through 131 removed outlier: 3.663A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 removed outlier: 3.539A pdb=" N VAL D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.623A pdb=" N ILE D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 189 through 198 removed outlier: 3.658A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.551A pdb=" N LYS D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.754A pdb=" N VAL D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.904A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.846A pdb=" N ARG D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 337 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.652A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 381 through 398 Processing helix chain 'D' and resid 403 through 427 Processing helix chain 'D' and resid 432 through 457 removed outlier: 5.141A pdb=" N ASP D 438 " --> pdb=" O HIS D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 548 through 562 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 596 through 609 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.681A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.528A pdb=" N LYS E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 84 removed outlier: 4.045A pdb=" N LYS E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.818A pdb=" N ALA E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 36 removed outlier: 4.386A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 86 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 66 through 83 removed outlier: 4.100A pdb=" N LYS G 72 " --> pdb=" O HIS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 removed outlier: 3.791A pdb=" N LEU G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.131A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.615A pdb=" N GLY H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 Processing helix chain 'I' and resid 81 through 91 removed outlier: 4.230A pdb=" N THR I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.696A pdb=" N ASN A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.646A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 67 Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.724A pdb=" N GLU A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.784A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.698A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.634A pdb=" N ILE A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.856A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.990A pdb=" N LYS A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.625A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.527A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 329 removed outlier: 3.987A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.576A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.665A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.835A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 removed outlier: 7.353A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 5.026A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.635A pdb=" N GLY A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.630A pdb=" N ALA A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 586 " --> pdb=" O MET A 582 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 removed outlier: 3.934A pdb=" N ASP A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 604 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 619 removed outlier: 3.509A pdb=" N LEU A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.600A pdb=" N GLN A 658 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 692 removed outlier: 3.745A pdb=" N GLN A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 708 removed outlier: 3.656A pdb=" N ILE A 700 " --> pdb=" O HIS A 696 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.522A pdb=" N ALA B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.744A pdb=" N ASN B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.772A pdb=" N VAL B 170 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 removed outlier: 3.514A pdb=" N PHE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 removed outlier: 3.729A pdb=" N VAL B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.895A pdb=" N ALA B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 284 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.178A pdb=" N ILE B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 removed outlier: 3.740A pdb=" N LYS B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 398 Processing helix chain 'B' and resid 403 through 427 removed outlier: 3.829A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 Processing helix chain 'B' and resid 460 through 478 removed outlier: 3.759A pdb=" N LEU B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 511 through 521 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 548 through 562 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 596 through 609 Processing helix chain 'B' and resid 617 through 624 Processing helix chain 'K' and resid -21 through -16 removed outlier: 3.685A pdb=" N LEU K -18 " --> pdb=" O ALA K -21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS K -17 " --> pdb=" O ASP K -20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS K -16 " --> pdb=" O HIS K -19 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid -21 through -16' Processing helix chain 'L' and resid -22 through -17 Processing sheet with id=AA1, first strand: chain 'C' and resid 510 through 513 removed outlier: 6.971A pdb=" N TYR C 510 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TRP J 33 " --> pdb=" O TYR C 510 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 512 " --> pdb=" O TRP J 33 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N TRP J 35 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 650 through 652 removed outlier: 6.838A pdb=" N VAL C 574 " --> pdb=" O PHE C 651 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS J 26 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'C' and resid 731 through 733 removed outlier: 3.588A pdb=" N GLU C 732 " --> pdb=" O SER C 742 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 742 " --> pdb=" O GLU C 732 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.739A pdb=" N GLY D 77 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 79 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 86 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 31 through 32 Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 18 Processing sheet with id=AA9, first strand: chain 'J' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 18 Processing sheet with id=AB3, first strand: chain 'H' and resid 44 through 45 Processing sheet with id=AB4, first strand: chain 'A' and resid 507 through 513 removed outlier: 7.839A pdb=" N TRP I 27 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N TYR A 510 " --> pdb=" O TRP I 27 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA I 29 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU A 512 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA I 31 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.541A pdb=" N PHE I 79 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 561 through 564 removed outlier: 3.640A pdb=" N VAL A 564 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 574 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AB8, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB9, first strand: chain 'B' and resid 40 through 42 1337 hydrogen bonds defined for protein. 3954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.80 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8702 1.34 - 1.46: 4992 1.46 - 1.58: 12829 1.58 - 1.70: 0 1.70 - 1.82: 284 Bond restraints: 26807 Sorted by residual: bond pdb=" N LYS A 659 " pdb=" CA LYS A 659 " ideal model delta sigma weight residual 1.453 1.471 -0.017 1.27e-02 6.20e+03 1.85e+00 bond pdb=" CA GLN J 92 " pdb=" CB GLN J 92 " ideal model delta sigma weight residual 1.527 1.559 -0.032 2.48e-02 1.63e+03 1.66e+00 bond pdb=" CG LEU D 416 " pdb=" CD2 LEU D 416 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" N ASP F 47 " pdb=" CA ASP F 47 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" N GLN A 332 " pdb=" CA GLN A 332 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 ... (remaining 26802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 36084 3.09 - 6.18: 141 6.18 - 9.27: 7 9.27 - 12.37: 0 12.37 - 15.46: 1 Bond angle restraints: 36233 Sorted by residual: angle pdb=" N THR A 655 " pdb=" CA THR A 655 " pdb=" C THR A 655 " ideal model delta sigma weight residual 111.71 106.48 5.23 1.15e+00 7.56e-01 2.06e+01 angle pdb=" CA LEU D 416 " pdb=" CB LEU D 416 " pdb=" CG LEU D 416 " ideal model delta sigma weight residual 116.30 131.76 -15.46 3.50e+00 8.16e-02 1.95e+01 angle pdb=" N VAL A 189 " pdb=" CA VAL A 189 " pdb=" C VAL A 189 " ideal model delta sigma weight residual 112.96 108.64 4.32 1.00e+00 1.00e+00 1.86e+01 angle pdb=" C TYR A 573 " pdb=" CA TYR A 573 " pdb=" CB TYR A 573 " ideal model delta sigma weight residual 115.89 110.48 5.41 1.32e+00 5.74e-01 1.68e+01 angle pdb=" C VAL D 415 " pdb=" N LEU D 416 " pdb=" CA LEU D 416 " ideal model delta sigma weight residual 120.31 114.48 5.83 1.52e+00 4.33e-01 1.47e+01 ... (remaining 36228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14470 17.80 - 35.60: 1497 35.60 - 53.40: 262 53.40 - 71.20: 61 71.20 - 89.00: 16 Dihedral angle restraints: 16306 sinusoidal: 6618 harmonic: 9688 Sorted by residual: dihedral pdb=" CA THR G 41 " pdb=" C THR G 41 " pdb=" N ILE G 42 " pdb=" CA ILE G 42 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA CYS C 266 " pdb=" C CYS C 266 " pdb=" N GLN C 267 " pdb=" CA GLN C 267 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASP C 633 " pdb=" CB ASP C 633 " pdb=" CG ASP C 633 " pdb=" OD1 ASP C 633 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 16303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2886 0.041 - 0.081: 954 0.081 - 0.122: 201 0.122 - 0.163: 26 0.163 - 0.204: 6 Chirality restraints: 4073 Sorted by residual: chirality pdb=" CB VAL C 482 " pdb=" CA VAL C 482 " pdb=" CG1 VAL C 482 " pdb=" CG2 VAL C 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU A 212 " pdb=" CB LEU A 212 " pdb=" CD1 LEU A 212 " pdb=" CD2 LEU A 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA ASP F 47 " pdb=" N ASP F 47 " pdb=" C ASP F 47 " pdb=" CB ASP F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 4070 not shown) Planarity restraints: 4655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 101 " 0.024 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP J 101 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP J 101 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP J 101 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 101 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 101 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 101 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 101 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 101 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP J 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 94 " -0.036 5.00e-02 4.00e+02 5.55e-02 4.94e+00 pdb=" N PRO I 95 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 267 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C GLN C 267 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN C 267 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN C 268 " -0.012 2.00e-02 2.50e+03 ... (remaining 4652 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 885 2.72 - 3.26: 27457 3.26 - 3.81: 44806 3.81 - 4.35: 54278 4.35 - 4.90: 91345 Nonbonded interactions: 218771 Sorted by model distance: nonbonded pdb=" OD1 ASP J 97 " pdb="ZN ZN J 202 " model vdw 2.173 2.230 nonbonded pdb=" OH TYR B 302 " pdb=" OE2 GLU B 333 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR B 449 " pdb=" O PRO B 497 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU C 635 " pdb=" OG SER C 637 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR C 235 " pdb=" O MET C 270 " model vdw 2.211 3.040 ... (remaining 218766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2)))) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 2 through 80 or resid 85 through 100)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 68.360 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26829 Z= 0.134 Angle : 0.560 15.457 36245 Z= 0.301 Chirality : 0.041 0.204 4073 Planarity : 0.004 0.056 4655 Dihedral : 14.841 88.999 10004 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3245 helix: 0.19 (0.12), residues: 1902 sheet: -2.31 (0.59), residues: 76 loop : -1.32 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP J 101 HIS 0.014 0.001 HIS E 35 PHE 0.016 0.001 PHE B 626 TYR 0.031 0.001 TYR A 544 ARG 0.005 0.000 ARG J 91 Details of bonding type rmsd hydrogen bonds : bond 0.13957 ( 1337) hydrogen bonds : angle 6.15406 ( 3954) metal coordination : bond 0.01015 ( 22) metal coordination : angle 3.05517 ( 12) covalent geometry : bond 0.00295 (26807) covalent geometry : angle 0.55725 (36233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8413 (t80) cc_final: 0.8007 (t80) REVERT: C 137 MET cc_start: 0.8191 (ttm) cc_final: 0.7903 (ttp) REVERT: C 365 MET cc_start: 0.7978 (mmm) cc_final: 0.7422 (mmt) REVERT: C 394 TYR cc_start: 0.8052 (t80) cc_final: 0.7776 (t80) REVERT: I 56 CYS cc_start: 0.5801 (m) cc_final: 0.5507 (m) REVERT: A 659 LYS cc_start: 0.3746 (OUTLIER) cc_final: 0.2969 (mmmt) REVERT: B 1 MET cc_start: 0.2284 (mtm) cc_final: 0.0520 (tpt) REVERT: B 465 CYS cc_start: 0.7359 (t) cc_final: 0.7080 (m) REVERT: B 530 ASN cc_start: 0.7011 (m-40) cc_final: 0.6405 (m-40) outliers start: 2 outliers final: 1 residues processed: 467 average time/residue: 0.4196 time to fit residues: 298.9627 Evaluate side-chains 281 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 chunk 164 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 474 HIS C 496 ASN C 697 ASN D 116 HIS ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS D 502 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 320 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 434 HIS B 470 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.252110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.206728 restraints weight = 35925.481| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 2.41 r_work: 0.4049 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26829 Z= 0.152 Angle : 0.551 8.583 36245 Z= 0.289 Chirality : 0.041 0.305 4073 Planarity : 0.004 0.099 4655 Dihedral : 4.653 80.473 3562 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.28 % Allowed : 7.67 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3245 helix: 0.50 (0.12), residues: 1955 sheet: -2.49 (0.57), residues: 76 loop : -1.35 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 101 HIS 0.014 0.001 HIS J 77 PHE 0.035 0.001 PHE B 260 TYR 0.020 0.001 TYR C 259 ARG 0.006 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 1337) hydrogen bonds : angle 4.64851 ( 3954) metal coordination : bond 0.01322 ( 22) metal coordination : angle 2.79423 ( 12) covalent geometry : bond 0.00349 (26807) covalent geometry : angle 0.54856 (36233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8782 (t80) cc_final: 0.8389 (t80) REVERT: C 109 ASN cc_start: 0.8674 (m-40) cc_final: 0.8432 (m110) REVERT: C 394 TYR cc_start: 0.8243 (t80) cc_final: 0.7962 (t80) REVERT: C 412 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5577 (tp30) REVERT: C 416 THR cc_start: 0.8732 (m) cc_final: 0.8504 (p) REVERT: C 496 ASN cc_start: 0.7247 (m-40) cc_final: 0.6982 (m110) REVERT: C 665 MET cc_start: 0.6233 (mmm) cc_final: 0.5643 (mpp) REVERT: D 171 ARG cc_start: 0.4259 (mmt180) cc_final: 0.4022 (mmm160) REVERT: J 67 GLU cc_start: 0.7791 (pm20) cc_final: 0.7526 (pm20) REVERT: H 43 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7519 (ptm160) REVERT: A 297 MET cc_start: 0.8335 (tpp) cc_final: 0.7762 (tpp) REVERT: A 476 MET cc_start: 0.8228 (mtm) cc_final: 0.8004 (mtt) REVERT: A 566 MET cc_start: 0.2157 (mmm) cc_final: 0.1344 (mtt) REVERT: A 657 MET cc_start: 0.3188 (OUTLIER) cc_final: 0.2867 (ttp) REVERT: B 1 MET cc_start: 0.3324 (mtm) cc_final: 0.0872 (tpt) REVERT: B 310 ASN cc_start: 0.8528 (t0) cc_final: 0.8297 (t0) REVERT: B 465 CYS cc_start: 0.8527 (t) cc_final: 0.7546 (m) REVERT: B 530 ASN cc_start: 0.7389 (m-40) cc_final: 0.6758 (m-40) outliers start: 37 outliers final: 23 residues processed: 324 average time/residue: 0.3942 time to fit residues: 206.5822 Evaluate side-chains 289 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 151 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 241 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 260 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS D 241 HIS D 345 HIS ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS A 264 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 377 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.246298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.197552 restraints weight = 36041.102| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 2.06 r_work: 0.4165 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26829 Z= 0.162 Angle : 0.539 11.506 36245 Z= 0.282 Chirality : 0.041 0.229 4073 Planarity : 0.004 0.050 4655 Dihedral : 4.608 82.330 3562 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.66 % Allowed : 10.09 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3245 helix: 0.60 (0.12), residues: 1950 sheet: -2.80 (0.47), residues: 92 loop : -1.33 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 101 HIS 0.011 0.001 HIS B 565 PHE 0.019 0.001 PHE A 493 TYR 0.027 0.001 TYR C 259 ARG 0.004 0.000 ARG B 603 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1337) hydrogen bonds : angle 4.43103 ( 3954) metal coordination : bond 0.01334 ( 22) metal coordination : angle 2.75444 ( 12) covalent geometry : bond 0.00382 (26807) covalent geometry : angle 0.53653 (36233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8684 (t80) cc_final: 0.8294 (t80) REVERT: C 109 ASN cc_start: 0.8622 (m-40) cc_final: 0.8370 (m110) REVERT: C 380 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6970 (mp0) REVERT: C 394 TYR cc_start: 0.8261 (t80) cc_final: 0.8032 (t80) REVERT: C 409 ASN cc_start: 0.7943 (t0) cc_final: 0.7595 (t0) REVERT: C 412 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5655 (tp30) REVERT: C 416 THR cc_start: 0.8671 (m) cc_final: 0.8446 (p) REVERT: C 496 ASN cc_start: 0.7335 (m-40) cc_final: 0.7051 (m110) REVERT: C 547 HIS cc_start: 0.6929 (t-90) cc_final: 0.6344 (t-90) REVERT: D 171 ARG cc_start: 0.3888 (OUTLIER) cc_final: 0.3438 (mmm160) REVERT: E 108 ASN cc_start: 0.8272 (t0) cc_final: 0.7947 (t0) REVERT: J 37 ILE cc_start: 0.7013 (tp) cc_final: 0.6738 (tp) REVERT: J 67 GLU cc_start: 0.7707 (pm20) cc_final: 0.7468 (pm20) REVERT: A 138 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 566 MET cc_start: 0.2286 (mmm) cc_final: 0.1528 (mtt) REVERT: A 605 MET cc_start: 0.7286 (pmm) cc_final: 0.6883 (pmm) REVERT: A 657 MET cc_start: 0.3405 (OUTLIER) cc_final: 0.3063 (ttp) REVERT: B 1 MET cc_start: 0.3018 (mtm) cc_final: 0.0725 (tpt) REVERT: B 358 MET cc_start: 0.8618 (mpp) cc_final: 0.8299 (mpp) REVERT: B 465 CYS cc_start: 0.8549 (t) cc_final: 0.7530 (m) REVERT: B 530 ASN cc_start: 0.7281 (m-40) cc_final: 0.6663 (m-40) outliers start: 48 outliers final: 32 residues processed: 304 average time/residue: 0.3688 time to fit residues: 181.5590 Evaluate side-chains 293 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain K residue -23 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 19 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 314 optimal weight: 0.3980 chunk 172 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 HIS D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.250491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.193922 restraints weight = 36733.605| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 2.46 r_work: 0.4095 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26829 Z= 0.141 Angle : 0.513 11.014 36245 Z= 0.268 Chirality : 0.040 0.213 4073 Planarity : 0.004 0.047 4655 Dihedral : 4.514 81.683 3562 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.80 % Allowed : 11.89 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3245 helix: 0.65 (0.12), residues: 1959 sheet: -2.80 (0.47), residues: 92 loop : -1.34 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 101 HIS 0.009 0.001 HIS B 565 PHE 0.020 0.001 PHE A 493 TYR 0.025 0.001 TYR A 544 ARG 0.006 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1337) hydrogen bonds : angle 4.30111 ( 3954) metal coordination : bond 0.01161 ( 22) metal coordination : angle 2.50800 ( 12) covalent geometry : bond 0.00330 (26807) covalent geometry : angle 0.51128 (36233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8736 (t80) cc_final: 0.8382 (t80) REVERT: C 394 TYR cc_start: 0.8226 (t80) cc_final: 0.8017 (t80) REVERT: C 409 ASN cc_start: 0.7934 (t0) cc_final: 0.7586 (t0) REVERT: C 412 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5946 (tp30) REVERT: C 496 ASN cc_start: 0.7452 (m-40) cc_final: 0.7214 (m110) REVERT: C 665 MET cc_start: 0.6294 (mmm) cc_final: 0.5596 (mpp) REVERT: D 171 ARG cc_start: 0.3843 (OUTLIER) cc_final: 0.3601 (mmm160) REVERT: D 371 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8639 (tp) REVERT: E 37 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (mp) REVERT: E 108 ASN cc_start: 0.8391 (t0) cc_final: 0.8008 (t0) REVERT: J 67 GLU cc_start: 0.7653 (pm20) cc_final: 0.7437 (pm20) REVERT: A 138 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: A 544 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: A 566 MET cc_start: 0.2420 (mmm) cc_final: 0.1687 (mtt) REVERT: A 605 MET cc_start: 0.7209 (pmm) cc_final: 0.6983 (pmm) REVERT: A 657 MET cc_start: 0.3617 (OUTLIER) cc_final: 0.3171 (ttp) REVERT: B 1 MET cc_start: 0.3027 (mtm) cc_final: 0.0736 (tpt) REVERT: B 358 MET cc_start: 0.8671 (mpp) cc_final: 0.8361 (mpp) REVERT: B 465 CYS cc_start: 0.8582 (t) cc_final: 0.7567 (m) REVERT: B 530 ASN cc_start: 0.7431 (m-40) cc_final: 0.6805 (m-40) outliers start: 52 outliers final: 32 residues processed: 307 average time/residue: 0.4809 time to fit residues: 241.0058 Evaluate side-chains 295 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 108 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 272 optimal weight: 30.0000 chunk 166 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS A 283 HIS A 334 ASN A 581 GLN B 369 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.249360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.192549 restraints weight = 36483.508| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.42 r_work: 0.4079 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26829 Z= 0.166 Angle : 0.527 12.138 36245 Z= 0.274 Chirality : 0.040 0.206 4073 Planarity : 0.004 0.045 4655 Dihedral : 4.493 82.116 3562 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 12.72 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3245 helix: 0.64 (0.12), residues: 1953 sheet: -3.11 (0.47), residues: 78 loop : -1.34 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 33 HIS 0.010 0.001 HIS B 565 PHE 0.019 0.001 PHE A 493 TYR 0.032 0.001 TYR A 544 ARG 0.005 0.000 ARG B 603 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1337) hydrogen bonds : angle 4.28498 ( 3954) metal coordination : bond 0.01326 ( 22) metal coordination : angle 2.65121 ( 12) covalent geometry : bond 0.00400 (26807) covalent geometry : angle 0.52529 (36233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8772 (t80) cc_final: 0.8375 (t80) REVERT: C 394 TYR cc_start: 0.8281 (t80) cc_final: 0.8078 (t80) REVERT: C 409 ASN cc_start: 0.7953 (t0) cc_final: 0.7580 (t0) REVERT: C 412 GLU cc_start: 0.6268 (mt-10) cc_final: 0.6053 (tp30) REVERT: C 496 ASN cc_start: 0.7444 (m-40) cc_final: 0.7210 (m110) REVERT: C 547 HIS cc_start: 0.7010 (t-90) cc_final: 0.6427 (t-90) REVERT: D 171 ARG cc_start: 0.3789 (OUTLIER) cc_final: 0.3341 (mmm160) REVERT: E 37 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8324 (mp) REVERT: E 108 ASN cc_start: 0.8407 (t0) cc_final: 0.8039 (t0) REVERT: J 67 GLU cc_start: 0.7630 (pm20) cc_final: 0.7419 (pm20) REVERT: H 53 ASP cc_start: 0.7278 (p0) cc_final: 0.7071 (p0) REVERT: A 138 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 297 MET cc_start: 0.8183 (tpp) cc_final: 0.7923 (tpt) REVERT: A 544 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.5663 (m-80) REVERT: A 566 MET cc_start: 0.2477 (mmm) cc_final: 0.1678 (mtt) REVERT: A 605 MET cc_start: 0.7139 (pmm) cc_final: 0.6885 (pmm) REVERT: A 657 MET cc_start: 0.3678 (OUTLIER) cc_final: 0.3338 (ttp) REVERT: B 1 MET cc_start: 0.3086 (mtm) cc_final: 0.0752 (tpt) REVERT: B 260 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6570 (t80) REVERT: B 358 MET cc_start: 0.8675 (mpp) cc_final: 0.8354 (mpp) REVERT: B 465 CYS cc_start: 0.8479 (t) cc_final: 0.7444 (m) REVERT: B 530 ASN cc_start: 0.7413 (m-40) cc_final: 0.6775 (m-40) outliers start: 64 outliers final: 44 residues processed: 310 average time/residue: 0.3701 time to fit residues: 189.4739 Evaluate side-chains 306 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 36 optimal weight: 6.9990 chunk 226 optimal weight: 0.3980 chunk 209 optimal weight: 0.5980 chunk 188 optimal weight: 0.5980 chunk 316 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C 264 HIS D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.239610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.187232 restraints weight = 35996.238| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.18 r_work: 0.3933 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26829 Z= 0.127 Angle : 0.514 11.244 36245 Z= 0.266 Chirality : 0.039 0.205 4073 Planarity : 0.003 0.045 4655 Dihedral : 4.402 81.297 3562 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.25 % Allowed : 13.61 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3245 helix: 0.76 (0.12), residues: 1939 sheet: -2.79 (0.57), residues: 62 loop : -1.33 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.014 0.001 HIS A 283 PHE 0.022 0.001 PHE C 350 TYR 0.031 0.001 TYR A 558 ARG 0.004 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 1337) hydrogen bonds : angle 4.19821 ( 3954) metal coordination : bond 0.01037 ( 22) metal coordination : angle 2.31255 ( 12) covalent geometry : bond 0.00293 (26807) covalent geometry : angle 0.51285 (36233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8815 (t80) cc_final: 0.8433 (t80) REVERT: C 236 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: C 380 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6899 (mp0) REVERT: C 496 ASN cc_start: 0.7475 (m-40) cc_final: 0.7238 (m110) REVERT: D 171 ARG cc_start: 0.3870 (OUTLIER) cc_final: 0.3521 (mmm160) REVERT: D 609 ASP cc_start: 0.7468 (t70) cc_final: 0.7174 (t70) REVERT: E 37 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8314 (mp) REVERT: E 108 ASN cc_start: 0.8424 (t0) cc_final: 0.8017 (t0) REVERT: A 138 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 544 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: A 560 CYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 566 MET cc_start: 0.2531 (mmm) cc_final: 0.1786 (mtt) REVERT: A 605 MET cc_start: 0.7229 (pmm) cc_final: 0.6980 (pmm) REVERT: A 657 MET cc_start: 0.3721 (ttt) cc_final: 0.3497 (ttp) REVERT: B 1 MET cc_start: 0.3180 (mtm) cc_final: 0.0868 (tpt) REVERT: B 213 ILE cc_start: 0.4553 (OUTLIER) cc_final: 0.4264 (pt) REVERT: B 260 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6708 (t80) REVERT: B 358 MET cc_start: 0.8636 (mpp) cc_final: 0.8302 (mpp) REVERT: B 461 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7278 (mt-10) REVERT: B 465 CYS cc_start: 0.8585 (t) cc_final: 0.7570 (m) REVERT: B 530 ASN cc_start: 0.7543 (m-40) cc_final: 0.6853 (m-40) outliers start: 65 outliers final: 41 residues processed: 312 average time/residue: 0.3566 time to fit residues: 181.3783 Evaluate side-chains 299 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 154 optimal weight: 0.3980 chunk 122 optimal weight: 0.1980 chunk 206 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 269 optimal weight: 20.0000 chunk 129 optimal weight: 0.0870 chunk 227 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 581 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.241158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.188124 restraints weight = 36188.343| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.16 r_work: 0.4078 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26829 Z= 0.114 Angle : 0.510 10.780 36245 Z= 0.263 Chirality : 0.039 0.215 4073 Planarity : 0.003 0.045 4655 Dihedral : 4.296 80.444 3559 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.42 % Allowed : 13.79 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3245 helix: 0.88 (0.12), residues: 1935 sheet: -2.65 (0.58), residues: 62 loop : -1.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.007 0.001 HIS A 283 PHE 0.020 0.001 PHE A 493 TYR 0.024 0.001 TYR A 544 ARG 0.003 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1337) hydrogen bonds : angle 4.12312 ( 3954) metal coordination : bond 0.00952 ( 22) metal coordination : angle 2.08386 ( 12) covalent geometry : bond 0.00259 (26807) covalent geometry : angle 0.50863 (36233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 267 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8760 (t80) cc_final: 0.8367 (t80) REVERT: C 297 MET cc_start: 0.8021 (tpp) cc_final: 0.7540 (mmm) REVERT: C 496 ASN cc_start: 0.7486 (m-40) cc_final: 0.7250 (m110) REVERT: D 171 ARG cc_start: 0.4012 (OUTLIER) cc_final: 0.3612 (mmm160) REVERT: D 609 ASP cc_start: 0.7258 (t70) cc_final: 0.6958 (t70) REVERT: E 108 ASN cc_start: 0.8316 (t0) cc_final: 0.7884 (t0) REVERT: A 75 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7060 (mtm180) REVERT: A 138 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: A 544 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.5958 (m-10) REVERT: A 560 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7896 (p) REVERT: A 566 MET cc_start: 0.2507 (mmm) cc_final: 0.1760 (mtt) REVERT: A 605 MET cc_start: 0.7114 (pmm) cc_final: 0.6841 (pmm) REVERT: B 1 MET cc_start: 0.3274 (mtm) cc_final: 0.0983 (tpt) REVERT: B 213 ILE cc_start: 0.4511 (OUTLIER) cc_final: 0.4233 (pt) REVERT: B 260 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6659 (t80) REVERT: B 465 CYS cc_start: 0.8351 (t) cc_final: 0.7315 (m) REVERT: B 530 ASN cc_start: 0.7361 (m-40) cc_final: 0.6783 (m110) outliers start: 70 outliers final: 40 residues processed: 308 average time/residue: 0.3681 time to fit residues: 184.5260 Evaluate side-chains 304 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 114 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 306 optimal weight: 0.0040 chunk 254 optimal weight: 3.9990 chunk 238 optimal weight: 0.3980 chunk 244 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 567 ASN D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.241358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.188273 restraints weight = 36054.454| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.24 r_work: 0.4062 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26829 Z= 0.119 Angle : 0.520 15.124 36245 Z= 0.266 Chirality : 0.039 0.238 4073 Planarity : 0.003 0.043 4655 Dihedral : 4.278 79.658 3559 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.07 % Allowed : 14.13 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3245 helix: 0.92 (0.12), residues: 1935 sheet: -2.69 (0.58), residues: 62 loop : -1.26 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 33 HIS 0.007 0.001 HIS A 283 PHE 0.023 0.001 PHE C 350 TYR 0.025 0.001 TYR A 544 ARG 0.007 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 1337) hydrogen bonds : angle 4.08486 ( 3954) metal coordination : bond 0.00969 ( 22) metal coordination : angle 2.01106 ( 12) covalent geometry : bond 0.00275 (26807) covalent geometry : angle 0.51879 (36233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8758 (t80) cc_final: 0.8450 (t80) REVERT: C 232 CYS cc_start: 0.7257 (t) cc_final: 0.6911 (p) REVERT: C 496 ASN cc_start: 0.7481 (m-40) cc_final: 0.7249 (m110) REVERT: D 102 GLU cc_start: 0.6039 (tm-30) cc_final: 0.5830 (pt0) REVERT: D 171 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.3543 (mmm160) REVERT: D 609 ASP cc_start: 0.7252 (t70) cc_final: 0.6950 (t70) REVERT: E 108 ASN cc_start: 0.8337 (t0) cc_final: 0.7896 (t0) REVERT: F 47 ASP cc_start: 0.7404 (m-30) cc_final: 0.6657 (t0) REVERT: A 75 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7057 (mtm180) REVERT: A 138 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: A 344 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 544 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6027 (m-80) REVERT: A 560 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 566 MET cc_start: 0.2491 (mmm) cc_final: 0.1757 (mtt) REVERT: A 605 MET cc_start: 0.7162 (pmm) cc_final: 0.6944 (pmm) REVERT: A 659 LYS cc_start: 0.3912 (OUTLIER) cc_final: 0.3375 (mmmt) REVERT: B 1 MET cc_start: 0.3297 (mtm) cc_final: 0.1006 (tpt) REVERT: B 260 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6719 (t80) REVERT: B 461 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 465 CYS cc_start: 0.8356 (t) cc_final: 0.7326 (m) REVERT: B 530 ASN cc_start: 0.7358 (m-40) cc_final: 0.6778 (m110) outliers start: 60 outliers final: 39 residues processed: 299 average time/residue: 0.3532 time to fit residues: 173.1786 Evaluate side-chains 302 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 169 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 319 optimal weight: 0.0000 chunk 292 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 243 optimal weight: 0.0980 chunk 164 optimal weight: 0.5980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.241868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.190116 restraints weight = 36083.353| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.13 r_work: 0.4062 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26829 Z= 0.105 Angle : 0.510 11.991 36245 Z= 0.261 Chirality : 0.039 0.267 4073 Planarity : 0.003 0.042 4655 Dihedral : 4.208 79.103 3559 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.87 % Allowed : 14.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3245 helix: 1.03 (0.12), residues: 1942 sheet: -2.68 (0.56), residues: 62 loop : -1.26 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.011 0.001 HIS A 283 PHE 0.020 0.001 PHE C 350 TYR 0.022 0.001 TYR A 544 ARG 0.004 0.000 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 1337) hydrogen bonds : angle 4.01020 ( 3954) metal coordination : bond 0.00848 ( 22) metal coordination : angle 1.86513 ( 12) covalent geometry : bond 0.00234 (26807) covalent geometry : angle 0.50919 (36233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8708 (t80) cc_final: 0.8401 (t80) REVERT: C 232 CYS cc_start: 0.7011 (t) cc_final: 0.6610 (p) REVERT: C 380 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6801 (mp0) REVERT: C 496 ASN cc_start: 0.7483 (m-40) cc_final: 0.7247 (m110) REVERT: D 102 GLU cc_start: 0.6061 (tm-30) cc_final: 0.5834 (tm-30) REVERT: D 171 ARG cc_start: 0.3850 (mmt180) cc_final: 0.3649 (mmm160) REVERT: D 253 LEU cc_start: 0.5031 (mm) cc_final: 0.4821 (mm) REVERT: D 437 MET cc_start: 0.5883 (tpt) cc_final: 0.5538 (tpt) REVERT: D 609 ASP cc_start: 0.7232 (t70) cc_final: 0.6943 (t70) REVERT: E 108 ASN cc_start: 0.8302 (t0) cc_final: 0.7833 (t0) REVERT: F 47 ASP cc_start: 0.7390 (m-30) cc_final: 0.6705 (t0) REVERT: A 75 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7148 (mtm180) REVERT: A 138 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: A 480 MET cc_start: 0.8380 (mmm) cc_final: 0.7996 (mmm) REVERT: A 544 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.5915 (m-10) REVERT: A 560 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 566 MET cc_start: 0.2550 (mmm) cc_final: 0.1842 (mtt) REVERT: A 659 LYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3397 (mmmt) REVERT: B 1 MET cc_start: 0.3318 (mtm) cc_final: 0.1077 (tpt) REVERT: B 213 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4206 (pt) REVERT: B 260 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6700 (t80) REVERT: B 465 CYS cc_start: 0.8274 (t) cc_final: 0.7329 (m) REVERT: B 530 ASN cc_start: 0.7313 (m-40) cc_final: 0.6703 (m110) outliers start: 54 outliers final: 39 residues processed: 308 average time/residue: 0.3592 time to fit residues: 180.8653 Evaluate side-chains 305 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 92 optimal weight: 6.9990 chunk 124 optimal weight: 0.0000 chunk 159 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 221 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.240375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.188030 restraints weight = 35744.451| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.20 r_work: 0.3943 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26829 Z= 0.132 Angle : 0.544 15.305 36245 Z= 0.276 Chirality : 0.040 0.269 4073 Planarity : 0.003 0.044 4655 Dihedral : 4.224 78.561 3559 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.83 % Allowed : 14.48 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3245 helix: 1.00 (0.12), residues: 1943 sheet: -2.77 (0.52), residues: 72 loop : -1.20 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 33 HIS 0.020 0.001 HIS A 283 PHE 0.030 0.001 PHE C 350 TYR 0.027 0.001 TYR A 544 ARG 0.006 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 1337) hydrogen bonds : angle 4.03553 ( 3954) metal coordination : bond 0.01085 ( 22) metal coordination : angle 2.08431 ( 12) covalent geometry : bond 0.00309 (26807) covalent geometry : angle 0.54238 (36233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8785 (t80) cc_final: 0.8478 (t80) REVERT: C 232 CYS cc_start: 0.7227 (t) cc_final: 0.6883 (p) REVERT: C 496 ASN cc_start: 0.7512 (m-40) cc_final: 0.7282 (m110) REVERT: C 566 MET cc_start: 0.6460 (mmp) cc_final: 0.4118 (pmm) REVERT: D 171 ARG cc_start: 0.3939 (OUTLIER) cc_final: 0.3483 (mmm160) REVERT: D 253 LEU cc_start: 0.5120 (mm) cc_final: 0.4908 (mm) REVERT: D 437 MET cc_start: 0.5972 (tpt) cc_final: 0.5209 (tpp) REVERT: D 609 ASP cc_start: 0.7407 (t70) cc_final: 0.7118 (t70) REVERT: E 108 ASN cc_start: 0.8426 (t0) cc_final: 0.7991 (t0) REVERT: F 47 ASP cc_start: 0.7572 (m-30) cc_final: 0.6783 (t0) REVERT: A 138 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 344 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8462 (mm) REVERT: A 544 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: A 560 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7982 (p) REVERT: A 566 MET cc_start: 0.2509 (mmm) cc_final: 0.1830 (mtt) REVERT: A 659 LYS cc_start: 0.3755 (OUTLIER) cc_final: 0.3200 (mmmt) REVERT: B 1 MET cc_start: 0.3321 (mtm) cc_final: 0.1031 (tpt) REVERT: B 213 ILE cc_start: 0.4519 (OUTLIER) cc_final: 0.4237 (pt) REVERT: B 260 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6746 (t80) REVERT: B 465 CYS cc_start: 0.8425 (t) cc_final: 0.7417 (m) REVERT: B 530 ASN cc_start: 0.7489 (m-40) cc_final: 0.6851 (m110) outliers start: 53 outliers final: 41 residues processed: 293 average time/residue: 0.3778 time to fit residues: 184.1028 Evaluate side-chains 304 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 184 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 HIS ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.228895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.174997 restraints weight = 35957.574| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.20 r_work: 0.3901 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26829 Z= 0.201 Angle : 0.592 11.514 36245 Z= 0.302 Chirality : 0.042 0.294 4073 Planarity : 0.004 0.046 4655 Dihedral : 4.368 79.432 3559 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.87 % Allowed : 14.75 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3245 helix: 0.78 (0.12), residues: 1958 sheet: -2.84 (0.52), residues: 72 loop : -1.25 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 101 HIS 0.038 0.001 HIS A 283 PHE 0.037 0.002 PHE C 350 TYR 0.038 0.002 TYR A 544 ARG 0.007 0.000 ARG B 603 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1337) hydrogen bonds : angle 4.18481 ( 3954) metal coordination : bond 0.01599 ( 22) metal coordination : angle 2.75925 ( 12) covalent geometry : bond 0.00489 (26807) covalent geometry : angle 0.58993 (36233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16442.54 seconds wall clock time: 289 minutes 0.57 seconds (17340.57 seconds total)