Starting phenix.real_space_refine on Fri Jul 26 06:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_37742_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_37742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_37742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_37742_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqe_37742/07_2024/8wqe_37742_neut.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 Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE -15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 13.46, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 10.33 Conformation dependent library (CDL) restraints added in 4.6 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: 2.92 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: 8.98 Time building geometry restraints manager: 11.29 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: 99.72 - 106.58: 618 106.58 - 113.44: 14798 113.44 - 120.30: 9830 120.30 - 127.16: 10724 127.16 - 134.02: 263 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 2.440 nonbonded pdb=" OH TYR B 449 " pdb=" O PRO B 497 " model vdw 2.200 2.440 nonbonded pdb=" OE2 GLU C 635 " pdb=" OG SER C 637 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR C 235 " pdb=" O MET C 270 " model vdw 2.211 2.440 ... (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 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 75.360 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.970 ------------------------------------------------------------------------------- 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 26807 Z= 0.191 Angle : 0.557 15.457 36233 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 2.985 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: 0.4211 time to fit residues: 301.2760 Evaluate side-chains 281 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 3.076 ------------------------------------------------------------------------------- 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: 6.9990 chunk 243 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 251 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS C 347 HIS C 362 GLN C 496 ASN C 697 ASN D 116 HIS D 345 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 ASN D 476 HIS ** D 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 320 HIS A 508 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 274 HIS B 434 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26807 Z= 0.397 Angle : 0.611 8.583 36233 Z= 0.320 Chirality : 0.044 0.322 4073 Planarity : 0.004 0.094 4655 Dihedral : 4.784 83.076 3562 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.66 % Allowed : 8.22 % Favored : 90.12 % 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: -0.67 (0.15), residues: 3245 helix: 0.29 (0.12), residues: 1947 sheet: -2.82 (0.49), residues: 92 loop : -1.36 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 101 HIS 0.018 0.001 HIS B 565 PHE 0.027 0.002 PHE B 260 TYR 0.034 0.002 TYR A 544 ARG 0.008 0.000 ARG D 379 *********************** 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 342 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 294 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8514 (t80) cc_final: 0.8073 (t80) REVERT: C 365 MET cc_start: 0.7869 (mmm) cc_final: 0.7468 (mmt) REVERT: C 394 TYR cc_start: 0.8168 (t80) cc_final: 0.7909 (t80) REVERT: E 108 ASN cc_start: 0.8146 (t0) cc_final: 0.7812 (t0) REVERT: A 151 MET cc_start: 0.8642 (tpp) cc_final: 0.8371 (ttt) REVERT: A 297 MET cc_start: 0.8060 (tpp) cc_final: 0.7727 (tpp) REVERT: A 566 MET cc_start: 0.2161 (mmm) cc_final: 0.1345 (mtt) REVERT: A 657 MET cc_start: 0.2912 (OUTLIER) cc_final: 0.2651 (ttp) REVERT: A 659 LYS cc_start: 0.3751 (OUTLIER) cc_final: 0.3153 (mmmt) REVERT: B 1 MET cc_start: 0.2257 (mtm) cc_final: 0.0403 (tpt) REVERT: B 530 ASN cc_start: 0.7048 (m-40) cc_final: 0.6470 (m-40) outliers start: 48 outliers final: 33 residues processed: 318 average time/residue: 0.3820 time to fit residues: 195.4434 Evaluate side-chains 290 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 3.015 ------------------------------------------------------------------------------- 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 375 VAL 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 G residue 47 SER Chi-restraints excluded: chain H residue 40 ASP 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 77 LEU 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 657 MET Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 399 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 292 optimal weight: 0.0270 chunk 315 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN C 496 ASN C 706 GLN 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 E 108 ASN A 264 HIS A 283 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26807 Z= 0.179 Angle : 0.507 12.467 36233 Z= 0.266 Chirality : 0.039 0.220 4073 Planarity : 0.004 0.048 4655 Dihedral : 4.571 81.131 3562 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.66 % Allowed : 11.30 % Favored : 87.04 % 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: -0.27 (0.15), residues: 3245 helix: 0.66 (0.12), residues: 1937 sheet: -2.45 (0.57), residues: 76 loop : -1.32 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 101 HIS 0.014 0.001 HIS A 283 PHE 0.018 0.001 PHE A 493 TYR 0.028 0.001 TYR C 259 ARG 0.004 0.000 ARG D 334 *********************** 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 329 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 281 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8489 (t80) cc_final: 0.8061 (t80) REVERT: E 108 ASN cc_start: 0.7960 (t0) cc_final: 0.7678 (t0) REVERT: J 37 ILE cc_start: 0.6747 (tp) cc_final: 0.6537 (tp) REVERT: A 138 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 297 MET cc_start: 0.7949 (tpp) cc_final: 0.7738 (tpp) REVERT: A 566 MET cc_start: 0.2224 (mmm) cc_final: 0.1517 (mtt) REVERT: A 605 MET cc_start: 0.6963 (pmm) cc_final: 0.6722 (pmm) REVERT: A 659 LYS cc_start: 0.3784 (OUTLIER) cc_final: 0.3179 (mmmt) REVERT: B 1 MET cc_start: 0.2348 (mtm) cc_final: 0.0536 (tpt) REVERT: B 358 MET cc_start: 0.7649 (mpp) cc_final: 0.7223 (mpp) REVERT: B 461 GLU cc_start: 0.6352 (pt0) cc_final: 0.6032 (pt0) REVERT: B 465 CYS cc_start: 0.7427 (t) cc_final: 0.7041 (m) REVERT: B 530 ASN cc_start: 0.7004 (m-40) cc_final: 0.6411 (m-40) outliers start: 48 outliers final: 33 residues processed: 307 average time/residue: 0.3514 time to fit residues: 177.1816 Evaluate side-chains 287 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 3.298 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 399 ASN 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 F residue 63 THR Chi-restraints excluded: chain J residue 92 GLN 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 200 LEU Chi-restraints excluded: chain A residue 248 ILE 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 561 THR 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 322 ASP 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 587 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 151 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN C 496 ASN D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 283 HIS A 581 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26807 Z= 0.265 Angle : 0.527 11.052 36233 Z= 0.276 Chirality : 0.040 0.217 4073 Planarity : 0.004 0.046 4655 Dihedral : 4.431 81.801 3559 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.28 % Allowed : 12.65 % 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: 0.63 (0.12), residues: 1938 sheet: -2.69 (0.52), residues: 86 loop : -1.31 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 101 HIS 0.013 0.001 HIS B 565 PHE 0.020 0.001 PHE A 493 TYR 0.030 0.001 TYR A 544 ARG 0.007 0.000 ARG D 63 *********************** 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 fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8519 (t80) cc_final: 0.8118 (t80) REVERT: E 37 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8221 (mp) REVERT: J 28 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.5482 (p0) REVERT: I 26 LYS cc_start: 0.6220 (ttmm) cc_final: 0.6015 (tttt) REVERT: A 297 MET cc_start: 0.7952 (tpp) cc_final: 0.7693 (tpp) REVERT: A 544 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5573 (m-80) REVERT: A 566 MET cc_start: 0.2334 (mmm) cc_final: 0.1630 (mtt) REVERT: A 659 LYS cc_start: 0.3737 (OUTLIER) cc_final: 0.3216 (mmmt) REVERT: B 1 MET cc_start: 0.2423 (mtm) cc_final: 0.0571 (tpt) REVERT: B 358 MET cc_start: 0.7834 (mpp) cc_final: 0.7111 (mpp) REVERT: B 461 GLU cc_start: 0.6358 (pt0) cc_final: 0.6029 (pt0) REVERT: B 465 CYS cc_start: 0.7487 (t) cc_final: 0.7082 (m) REVERT: B 530 ASN cc_start: 0.7030 (m-40) cc_final: 0.6425 (m-40) outliers start: 66 outliers final: 46 residues processed: 301 average time/residue: 0.3442 time to fit residues: 169.6144 Evaluate side-chains 296 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 246 time to evaluate : 3.048 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 399 ASN 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 90 ILE 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 63 THR Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 92 GLN 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 H residue 64 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 77 LEU 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 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 ASP 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 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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 577 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 231 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 264 optimal weight: 9.9990 chunk 214 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS C 313 GLN C 496 ASN D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS A 283 HIS A 334 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26807 Z= 0.178 Angle : 0.501 13.933 36233 Z= 0.259 Chirality : 0.039 0.208 4073 Planarity : 0.003 0.045 4655 Dihedral : 4.362 80.191 3559 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.11 % Allowed : 13.93 % Favored : 83.97 % 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: -0.10 (0.15), residues: 3245 helix: 0.79 (0.12), residues: 1947 sheet: -2.45 (0.58), residues: 76 loop : -1.26 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 33 HIS 0.009 0.001 HIS D 476 PHE 0.022 0.001 PHE C 350 TYR 0.024 0.001 TYR A 558 ARG 0.003 0.000 ARG A 302 *********************** 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 329 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 268 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8526 (t80) cc_final: 0.8092 (t80) REVERT: D 171 ARG cc_start: 0.4276 (mmm160) cc_final: 0.3915 (mmp80) REVERT: D 396 ILE cc_start: 0.8380 (mm) cc_final: 0.8095 (mm) REVERT: E 37 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8156 (mp) REVERT: J 28 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5512 (p0) REVERT: A 297 MET cc_start: 0.7956 (tpp) cc_final: 0.7707 (tpp) REVERT: A 544 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5623 (m-80) REVERT: A 566 MET cc_start: 0.2307 (mmm) cc_final: 0.1623 (mtt) REVERT: A 659 LYS cc_start: 0.3773 (OUTLIER) cc_final: 0.3241 (mmmt) REVERT: B 1 MET cc_start: 0.2437 (mtm) cc_final: 0.0617 (tpt) REVERT: B 358 MET cc_start: 0.7865 (mpp) cc_final: 0.7253 (mpp) REVERT: B 465 CYS cc_start: 0.7451 (t) cc_final: 0.7050 (m) REVERT: B 530 ASN cc_start: 0.7017 (m-40) cc_final: 0.6385 (m-40) outliers start: 61 outliers final: 42 residues processed: 304 average time/residue: 0.3487 time to fit residues: 174.4855 Evaluate side-chains 292 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 MET 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 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 399 ASN 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 105 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 92 GLN 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 200 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL 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 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 ASP 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 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 chunk 61 optimal weight: 0.0070 chunk 182 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 310 optimal weight: 0.0070 chunk 257 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN C 496 ASN D 116 HIS D 394 GLN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 581 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26807 Z= 0.198 Angle : 0.505 11.323 36233 Z= 0.262 Chirality : 0.039 0.207 4073 Planarity : 0.003 0.046 4655 Dihedral : 4.329 79.910 3559 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.66 % Allowed : 14.20 % Favored : 83.14 % 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: -0.06 (0.15), residues: 3245 helix: 0.83 (0.12), residues: 1949 sheet: -2.70 (0.60), residues: 62 loop : -1.27 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 33 HIS 0.011 0.001 HIS A 283 PHE 0.030 0.001 PHE A 112 TYR 0.032 0.001 TYR A 558 ARG 0.004 0.000 ARG B 603 *********************** 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 349 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 3.217 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: 0.8522 (t80) cc_final: 0.8092 (t80) REVERT: D 396 ILE cc_start: 0.8285 (mm) cc_final: 0.7960 (mm) REVERT: D 609 ASP cc_start: 0.6109 (t70) cc_final: 0.5864 (t70) REVERT: E 37 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8161 (mp) REVERT: J 28 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5463 (p0) REVERT: J 37 ILE cc_start: 0.6694 (tp) cc_final: 0.6443 (tp) REVERT: A 297 MET cc_start: 0.7963 (tpp) cc_final: 0.7705 (tpp) REVERT: A 544 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: A 566 MET cc_start: 0.2279 (mmm) cc_final: 0.1606 (mtt) REVERT: A 659 LYS cc_start: 0.3823 (OUTLIER) cc_final: 0.3302 (mmmt) REVERT: B 1 MET cc_start: 0.2483 (mtm) cc_final: 0.0684 (tpt) REVERT: B 213 ILE cc_start: 0.3807 (OUTLIER) cc_final: 0.3428 (pt) REVERT: B 358 MET cc_start: 0.7934 (mpp) cc_final: 0.7327 (mpp) REVERT: B 465 CYS cc_start: 0.7486 (t) cc_final: 0.7051 (m) REVERT: B 530 ASN cc_start: 0.7005 (m-40) cc_final: 0.6329 (m-40) outliers start: 77 outliers final: 47 residues processed: 322 average time/residue: 0.3357 time to fit residues: 178.1982 Evaluate side-chains 307 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 255 time to evaluate : 2.778 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 548 ASP 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 63 THR Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 99 ILE 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 I residue 69 THR 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 544 TYR 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 201 ASP Chi-restraints excluded: chain B residue 213 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 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 226 optimal weight: 0.0970 chunk 175 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 193 optimal weight: 0.2980 chunk 188 optimal weight: 0.2980 chunk 142 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN C 496 ASN D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26807 Z= 0.161 Angle : 0.505 10.737 36233 Z= 0.260 Chirality : 0.038 0.208 4073 Planarity : 0.003 0.045 4655 Dihedral : 4.287 78.814 3559 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % Favored : 82.69 % 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: 0.04 (0.15), residues: 3245 helix: 0.93 (0.12), residues: 1952 sheet: -2.72 (0.60), residues: 62 loop : -1.24 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 33 HIS 0.014 0.001 HIS A 283 PHE 0.033 0.001 PHE B 260 TYR 0.021 0.001 TYR A 544 ARG 0.007 0.000 ARG D 171 *********************** 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 340 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 272 time to evaluate : 2.939 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: 0.8494 (t80) cc_final: 0.8071 (t80) REVERT: D 609 ASP cc_start: 0.6088 (t70) cc_final: 0.5852 (t70) REVERT: E 37 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 544 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: A 566 MET cc_start: 0.2318 (mmm) cc_final: 0.1647 (mtt) REVERT: A 659 LYS cc_start: 0.3881 (OUTLIER) cc_final: 0.3363 (mmmt) REVERT: B 1 MET cc_start: 0.2511 (mtm) cc_final: 0.0775 (tpt) REVERT: B 213 ILE cc_start: 0.3753 (OUTLIER) cc_final: 0.3395 (pt) REVERT: B 358 MET cc_start: 0.7927 (mpp) cc_final: 0.7372 (mpp) REVERT: B 465 CYS cc_start: 0.7457 (t) cc_final: 0.7052 (m) REVERT: B 530 ASN cc_start: 0.6988 (m-40) cc_final: 0.6283 (m-40) outliers start: 68 outliers final: 45 residues processed: 308 average time/residue: 0.3479 time to fit residues: 175.9161 Evaluate side-chains 307 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 2.871 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 548 ASP 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 63 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 69 THR 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 200 LEU Chi-restraints excluded: chain A residue 271 VAL 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 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 213 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 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 196 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 243 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 ASN D 116 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26807 Z= 0.177 Angle : 0.518 14.889 36233 Z= 0.263 Chirality : 0.039 0.241 4073 Planarity : 0.003 0.043 4655 Dihedral : 4.255 78.551 3559 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.18 % Allowed : 15.31 % Favored : 82.52 % 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: 0.08 (0.15), residues: 3245 helix: 0.97 (0.12), residues: 1956 sheet: -2.68 (0.60), residues: 62 loop : -1.26 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 33 HIS 0.007 0.001 HIS B 565 PHE 0.034 0.001 PHE A 112 TYR 0.023 0.001 TYR A 544 ARG 0.003 0.000 ARG B 603 *********************** 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 333 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 270 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8489 (t80) cc_final: 0.8136 (t80) REVERT: D 609 ASP cc_start: 0.6059 (t70) cc_final: 0.5834 (t70) REVERT: E 37 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 75 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6332 (mtm-85) REVERT: A 344 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 544 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: A 566 MET cc_start: 0.2467 (mmm) cc_final: 0.1784 (mtt) REVERT: A 659 LYS cc_start: 0.3953 (OUTLIER) cc_final: 0.3427 (mmmt) REVERT: B 1 MET cc_start: 0.2494 (mtm) cc_final: 0.0779 (tpt) REVERT: B 213 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3350 (pt) REVERT: B 358 MET cc_start: 0.7949 (mpp) cc_final: 0.7349 (mpp) REVERT: B 465 CYS cc_start: 0.7437 (t) cc_final: 0.7027 (m) REVERT: B 530 ASN cc_start: 0.6974 (m-40) cc_final: 0.6408 (m110) outliers start: 63 outliers final: 49 residues processed: 306 average time/residue: 0.3363 time to fit residues: 170.1953 Evaluate side-chains 316 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 2.909 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 548 ASP 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 63 THR Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 69 THR 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 191 VAL 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 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 561 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 213 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 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 270 optimal weight: 50.0000 chunk 288 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 226 optimal weight: 0.0670 chunk 88 optimal weight: 0.8980 chunk 260 optimal weight: 0.0470 chunk 272 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 ASN D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26807 Z= 0.192 Angle : 0.528 11.680 36233 Z= 0.269 Chirality : 0.039 0.278 4073 Planarity : 0.003 0.044 4655 Dihedral : 4.262 78.341 3559 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.38 % Allowed : 15.20 % Favored : 82.41 % 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: 0.09 (0.15), residues: 3245 helix: 0.96 (0.12), residues: 1959 sheet: -2.70 (0.59), residues: 62 loop : -1.25 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 555 HIS 0.012 0.001 HIS A 283 PHE 0.035 0.001 PHE A 112 TYR 0.024 0.001 TYR A 544 ARG 0.003 0.000 ARG B 603 *********************** 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 335 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8532 (t80) cc_final: 0.8171 (t80) REVERT: C 566 MET cc_start: 0.3606 (mmp) cc_final: 0.3109 (pmm) REVERT: D 609 ASP cc_start: 0.6076 (t70) cc_final: 0.5849 (t70) REVERT: E 37 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 75 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6337 (mtm-85) REVERT: A 344 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (mm) REVERT: A 544 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: A 566 MET cc_start: 0.2461 (mmm) cc_final: 0.1790 (mtt) REVERT: A 659 LYS cc_start: 0.3932 (OUTLIER) cc_final: 0.3427 (mmmt) REVERT: B 1 MET cc_start: 0.2444 (mtm) cc_final: 0.0769 (tpt) REVERT: B 213 ILE cc_start: 0.3739 (OUTLIER) cc_final: 0.3374 (pt) REVERT: B 220 MET cc_start: 0.4506 (mpp) cc_final: 0.3770 (mpp) REVERT: B 358 MET cc_start: 0.7970 (mpp) cc_final: 0.7396 (mpp) REVERT: B 465 CYS cc_start: 0.7408 (t) cc_final: 0.7008 (m) REVERT: B 530 ASN cc_start: 0.6975 (m-40) cc_final: 0.6410 (m110) outliers start: 69 outliers final: 55 residues processed: 303 average time/residue: 0.3405 time to fit residues: 170.8765 Evaluate side-chains 323 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 262 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 200 LEU 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 297 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 548 ASP 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 63 THR Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 69 THR 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 191 VAL 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 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 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 201 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 343 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 186 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 319 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 156 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 ASN D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS J 77 HIS A 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26807 Z= 0.189 Angle : 0.538 15.660 36233 Z= 0.274 Chirality : 0.039 0.271 4073 Planarity : 0.003 0.044 4655 Dihedral : 4.264 78.132 3559 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.28 % Allowed : 15.69 % Favored : 82.03 % 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: 0.08 (0.15), residues: 3245 helix: 0.96 (0.12), residues: 1960 sheet: -2.77 (0.59), residues: 62 loop : -1.24 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 101 HIS 0.018 0.001 HIS A 283 PHE 0.038 0.001 PHE C 350 TYR 0.024 0.001 TYR A 544 ARG 0.004 0.000 ARG A 287 ********************** 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 332 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 TYR cc_start: 0.8529 (t80) cc_final: 0.8168 (t80) REVERT: C 566 MET cc_start: 0.3580 (mmp) cc_final: 0.3093 (pmm) REVERT: D 609 ASP cc_start: 0.6071 (t70) cc_final: 0.5855 (t70) REVERT: E 37 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 75 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6331 (mtm-85) REVERT: A 297 MET cc_start: 0.7922 (tpp) cc_final: 0.7655 (tpp) REVERT: A 344 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 544 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: A 566 MET cc_start: 0.2456 (mmm) cc_final: 0.1799 (mtt) REVERT: A 659 LYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3431 (mmmt) REVERT: B 1 MET cc_start: 0.2437 (mtm) cc_final: 0.0771 (tpt) REVERT: B 213 ILE cc_start: 0.3726 (OUTLIER) cc_final: 0.3366 (pt) REVERT: B 358 MET cc_start: 0.7977 (mpp) cc_final: 0.7422 (mpp) REVERT: B 465 CYS cc_start: 0.7413 (t) cc_final: 0.7008 (m) REVERT: B 530 ASN cc_start: 0.6971 (m-40) cc_final: 0.6408 (m110) outliers start: 66 outliers final: 55 residues processed: 301 average time/residue: 0.3411 time to fit residues: 169.8369 Evaluate side-chains 322 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 261 time to evaluate : 3.176 ------------------------------------------------------------------------------- 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 297 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 548 ASP 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 63 THR Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 69 THR 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 191 VAL 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 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 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 201 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 TYR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 481 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 234 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 GLN C 362 GLN ** C 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS B 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.224340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.4220 r_free = 0.4220 target = 0.167570 restraints weight = 35811.709| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.85 r_work: 0.3945 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26807 Z= 0.245 Angle : 0.552 12.544 36233 Z= 0.281 Chirality : 0.040 0.277 4073 Planarity : 0.004 0.045 4655 Dihedral : 4.315 78.658 3559 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.49 % Allowed : 15.48 % Favored : 82.03 % 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: 0.01 (0.15), residues: 3245 helix: 0.89 (0.12), residues: 1956 sheet: -2.93 (0.53), residues: 72 loop : -1.22 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 33 HIS 0.029 0.001 HIS J 77 PHE 0.047 0.002 PHE B 260 TYR 0.028 0.001 TYR A 544 ARG 0.005 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.71 seconds wall clock time: 106 minutes 20.98 seconds (6380.98 seconds total)