Starting phenix.real_space_refine on Fri Mar 22 09:44:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6i_33022/03_2024/7x6i_33022_trim.pdb" } resolution = 3.93 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= 0.038 sd= 0.165 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 180 5.16 5 C 21256 2.51 5 N 5396 2.21 5 O 6008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32864 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "C" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "D" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1282 SG CYS A 176 49.195 110.784 101.540 1.00 99.11 S ATOM 1296 SG CYS A 178 45.896 110.787 99.609 1.00106.36 S ATOM 1318 SG CYS A 181 48.495 108.134 98.810 1.00 97.79 S ATOM 9350 SG CYS B 176 56.766 49.195 101.540 1.00 99.11 S ATOM 9364 SG CYS B 178 56.763 45.896 99.609 1.00106.36 S ATOM 9386 SG CYS B 181 59.416 48.495 98.810 1.00 97.79 S ATOM 14938 SG CYS C 176 118.357 56.766 101.540 1.00 99.11 S ATOM 14952 SG CYS C 178 121.656 56.763 99.609 1.00106.36 S ATOM 14974 SG CYS C 181 119.057 59.416 98.810 1.00 97.79 S ATOM 20526 SG CYS D 176 110.786 118.357 101.540 1.00 99.11 S ATOM 20540 SG CYS D 178 110.789 121.656 99.609 1.00106.36 S ATOM 20562 SG CYS D 181 108.136 119.057 98.810 1.00 97.79 S Time building chain proxies: 16.16, per 1000 atoms: 0.49 Number of scatterers: 32864 At special positions: 0 Unit cell: (168.64, 168.64, 177.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 180 16.00 P 16 15.00 O 6008 8.00 N 5396 7.00 C 21256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 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: 13.07 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 181 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 181 " pdb=" ZN C 803 " pdb="ZN ZN C 803 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 181 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 181 " Number of angles added : 12 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 8 sheets defined 70.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 58 removed outlier: 4.044A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 753 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.226A pdb=" N GLY E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS E 213 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 241 through 256 Processing helix chain 'E' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 257 through 260' Processing helix chain 'E' and resid 270 through 279 removed outlier: 4.163A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 636 through 648 Processing helix chain 'B' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 753 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 585 through 589 Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 636 through 648 Processing helix chain 'C' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 753 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 585 through 589 Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 636 through 648 Processing helix chain 'D' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 731 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 753 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 170 through 176 Processing helix chain 'F' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 212 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 215 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 241 through 256 Processing helix chain 'F' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 328 through 347 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 143 through 146 Processing helix chain 'G' and resid 151 through 158 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 212 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS G 213 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 215 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'G' and resid 241 through 256 Processing helix chain 'G' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'G' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 286 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 328 through 347 Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 143 through 146 Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 170 through 176 Processing helix chain 'H' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE H 212 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 213 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'H' and resid 241 through 256 Processing helix chain 'H' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 286 Processing helix chain 'H' and resid 295 through 309 Processing helix chain 'H' and resid 328 through 347 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.598A pdb=" N ILE B 168 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.602A pdb=" N ILE A 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL E 34 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE E 199 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E 36 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 201 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU E 38 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS E 35 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 222 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 37 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS E 224 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 39 " --> pdb=" O CYS E 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA E 226 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE E 264 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS E 322 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 266 " --> pdb=" O HIS E 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.600A pdb=" N ILE C 168 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.600A pdb=" N ILE D 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL F 34 " --> pdb=" O LYS F 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 199 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE F 222 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU F 39 " --> pdb=" O CYS F 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 264 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS F 322 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU F 266 " --> pdb=" O HIS F 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL G 34 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE G 199 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU G 36 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL G 201 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 38 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS G 35 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE G 222 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 37 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU G 39 " --> pdb=" O CYS G 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA G 226 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE G 264 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS G 322 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU G 266 " --> pdb=" O HIS G 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL H 34 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE H 199 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU H 36 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 201 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU H 38 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS H 35 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE H 222 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU H 37 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS H 224 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU H 39 " --> pdb=" O CYS H 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA H 226 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE H 264 " --> pdb=" O TYR H 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS H 322 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU H 266 " --> pdb=" O HIS H 322 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5448 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: 11.95 Time building geometry restraints manager: 14.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5746 1.32 - 1.45: 8730 1.45 - 1.58: 18748 1.58 - 1.70: 68 1.70 - 1.83: 284 Bond restraints: 33576 Sorted by residual: bond pdb=" C SER F 263 " pdb=" N ILE F 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER G 263 " pdb=" N ILE G 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER H 263 " pdb=" N ILE H 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER E 263 " pdb=" N ILE E 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" CA VAL E 50 " pdb=" CB VAL E 50 " ideal model delta sigma weight residual 1.540 1.597 -0.057 1.25e-02 6.40e+03 2.08e+01 ... (remaining 33571 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.28: 503 105.28 - 112.54: 16763 112.54 - 119.81: 12694 119.81 - 127.07: 15065 127.07 - 134.34: 395 Bond angle restraints: 45420 Sorted by residual: angle pdb=" C ASP E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta sigma weight residual 120.00 111.68 8.32 1.10e+00 8.26e-01 5.72e+01 angle pdb=" C ASP F 133 " pdb=" N GLY F 134 " pdb=" CA GLY F 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" C ASP G 133 " pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" C ASP H 133 " pdb=" N GLY H 134 " pdb=" CA GLY H 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" O ASP F 133 " pdb=" C ASP F 133 " pdb=" N GLY F 134 " ideal model delta sigma weight residual 122.86 131.65 -8.79 1.18e+00 7.18e-01 5.54e+01 ... (remaining 45415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 19812 34.98 - 69.96: 504 69.96 - 104.93: 32 104.93 - 139.91: 28 139.91 - 174.89: 12 Dihedral angle restraints: 20388 sinusoidal: 8660 harmonic: 11728 Sorted by residual: dihedral pdb=" C8 GTP H 401 " pdb=" C1' GTP H 401 " pdb=" N9 GTP H 401 " pdb=" O4' GTP H 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C8 GTP G 401 " pdb=" C1' GTP G 401 " pdb=" N9 GTP G 401 " pdb=" O4' GTP G 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C8 GTP F 401 " pdb=" C1' GTP F 401 " pdb=" N9 GTP F 401 " pdb=" O4' GTP F 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 20385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4147 0.077 - 0.154: 746 0.154 - 0.232: 159 0.232 - 0.309: 16 0.309 - 0.386: 12 Chirality restraints: 5080 Sorted by residual: chirality pdb=" CA GLU G 58 " pdb=" N GLU G 58 " pdb=" C GLU G 58 " pdb=" CB GLU G 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA GLU H 58 " pdb=" N GLU H 58 " pdb=" C GLU H 58 " pdb=" CB GLU H 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA GLU F 58 " pdb=" N GLU F 58 " pdb=" C GLU F 58 " pdb=" CB GLU F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5077 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 805 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY B 805 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY B 805 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY B 805 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY C 805 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY C 805 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY C 805 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY C 805 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY A 806 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY A 806 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY A 806 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY A 806 " -0.088 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 9220 2.82 - 3.34: 31875 3.34 - 3.86: 54356 3.86 - 4.38: 61661 4.38 - 4.90: 106218 Nonbonded interactions: 263330 Sorted by model distance: nonbonded pdb=" O ILE D 209 " pdb=" OG SER D 213 " model vdw 2.306 2.440 nonbonded pdb=" O ILE A 209 " pdb=" OG SER A 213 " model vdw 2.306 2.440 nonbonded pdb=" O ILE B 209 " pdb=" OG SER B 213 " model vdw 2.306 2.440 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.315 2.440 ... (remaining 263325 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' and (resid 16 through 753 or resid 801 through 804)) selection = (chain 'B' and (resid 16 through 753 or resid 801 through 804)) selection = (chain 'C' and (resid 16 through 753 or resid 801 through 804)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.840 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 87.890 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.230 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.008 0.119 33576 Z= 0.535 Angle : 1.056 10.648 45420 Z= 0.626 Chirality : 0.066 0.386 5080 Planarity : 0.007 0.088 5652 Dihedral : 16.754 174.890 12760 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.45 % Allowed : 2.37 % Favored : 97.18 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.12), residues: 3928 helix: 0.10 (0.09), residues: 2516 sheet: -1.41 (0.48), residues: 116 loop : -0.81 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 327 HIS 0.006 0.001 HIS E 322 PHE 0.051 0.003 PHE D 540 TYR 0.024 0.003 TYR G 155 ARG 0.022 0.001 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 516 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7898 (mmm) cc_final: 0.7540 (tpt) REVERT: A 87 GLU cc_start: 0.8208 (tp30) cc_final: 0.7689 (tp30) REVERT: A 88 LEU cc_start: 0.9431 (tp) cc_final: 0.9225 (tp) REVERT: A 90 LEU cc_start: 0.9328 (tp) cc_final: 0.8988 (tp) REVERT: A 636 ASP cc_start: 0.8399 (t70) cc_final: 0.8169 (t0) REVERT: E 57 HIS cc_start: 0.6041 (m90) cc_final: 0.5592 (m170) REVERT: E 240 MET cc_start: 0.7488 (tpt) cc_final: 0.6866 (tpt) REVERT: E 243 MET cc_start: 0.7446 (tpp) cc_final: 0.6896 (tpp) REVERT: E 258 TRP cc_start: 0.7825 (m100) cc_final: 0.7152 (m100) REVERT: E 286 CYS cc_start: 0.7511 (t) cc_final: 0.7152 (t) REVERT: B 66 MET cc_start: 0.7900 (mmm) cc_final: 0.7536 (tpt) REVERT: B 87 GLU cc_start: 0.8211 (tp30) cc_final: 0.7692 (tp30) REVERT: B 88 LEU cc_start: 0.9427 (tp) cc_final: 0.9221 (tp) REVERT: B 90 LEU cc_start: 0.9327 (tp) cc_final: 0.8986 (tp) REVERT: B 636 ASP cc_start: 0.8403 (t70) cc_final: 0.8168 (t0) REVERT: C 66 MET cc_start: 0.7906 (mmm) cc_final: 0.7544 (tpt) REVERT: C 87 GLU cc_start: 0.8205 (tp30) cc_final: 0.7691 (tp30) REVERT: C 88 LEU cc_start: 0.9430 (tp) cc_final: 0.9225 (tp) REVERT: C 90 LEU cc_start: 0.9332 (tp) cc_final: 0.8985 (tp) REVERT: C 636 ASP cc_start: 0.8403 (t70) cc_final: 0.8171 (t0) REVERT: D 66 MET cc_start: 0.7896 (mmm) cc_final: 0.7533 (tpt) REVERT: D 87 GLU cc_start: 0.8215 (tp30) cc_final: 0.7694 (tp30) REVERT: D 88 LEU cc_start: 0.9431 (tp) cc_final: 0.9224 (tp) REVERT: D 90 LEU cc_start: 0.9329 (tp) cc_final: 0.8986 (tp) REVERT: D 636 ASP cc_start: 0.8400 (t70) cc_final: 0.8165 (t0) REVERT: F 57 HIS cc_start: 0.6071 (m90) cc_final: 0.5595 (m170) REVERT: F 240 MET cc_start: 0.7472 (tpt) cc_final: 0.6823 (tpt) REVERT: F 243 MET cc_start: 0.7425 (tpp) cc_final: 0.6846 (tpp) REVERT: F 258 TRP cc_start: 0.7859 (m100) cc_final: 0.7171 (m100) REVERT: F 286 CYS cc_start: 0.7481 (t) cc_final: 0.7126 (t) REVERT: G 57 HIS cc_start: 0.6079 (m90) cc_final: 0.5613 (m170) REVERT: G 240 MET cc_start: 0.7487 (tpt) cc_final: 0.6835 (tpt) REVERT: G 243 MET cc_start: 0.7441 (tpp) cc_final: 0.6865 (tpp) REVERT: G 258 TRP cc_start: 0.7863 (m100) cc_final: 0.7175 (m100) REVERT: G 286 CYS cc_start: 0.7491 (t) cc_final: 0.7127 (t) REVERT: H 57 HIS cc_start: 0.6084 (m90) cc_final: 0.5614 (m170) REVERT: H 240 MET cc_start: 0.7470 (tpt) cc_final: 0.6824 (tpt) REVERT: H 243 MET cc_start: 0.7426 (tpp) cc_final: 0.6851 (tpp) REVERT: H 258 TRP cc_start: 0.7883 (m100) cc_final: 0.7198 (m100) REVERT: H 286 CYS cc_start: 0.7488 (t) cc_final: 0.7130 (t) outliers start: 16 outliers final: 4 residues processed: 524 average time/residue: 0.4469 time to fit residues: 375.2319 Evaluate side-chains 360 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 356 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS E 306 GLN B 192 HIS ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS F 306 GLN G 244 HIS G 306 GLN H 244 HIS H 306 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 33576 Z= 0.480 Angle : 0.720 8.514 45420 Z= 0.371 Chirality : 0.045 0.166 5080 Planarity : 0.004 0.040 5652 Dihedral : 13.034 153.577 4916 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.47 % Allowed : 7.38 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.13), residues: 3928 helix: 1.25 (0.10), residues: 2556 sheet: -1.20 (0.40), residues: 152 loop : -0.49 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 315 HIS 0.005 0.001 HIS E 244 PHE 0.018 0.003 PHE A 565 TYR 0.024 0.002 TYR D 118 ARG 0.004 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 414 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7834 (mmm) cc_final: 0.7512 (tpt) REVERT: A 87 GLU cc_start: 0.8310 (tp30) cc_final: 0.7652 (tp30) REVERT: A 212 SER cc_start: 0.9057 (m) cc_final: 0.8586 (p) REVERT: A 422 MET cc_start: 0.7659 (ttm) cc_final: 0.7355 (ttt) REVERT: A 711 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7824 (tp40) REVERT: E 38 LEU cc_start: 0.8279 (mp) cc_final: 0.7986 (mt) REVERT: E 240 MET cc_start: 0.7876 (tpt) cc_final: 0.7574 (tpt) REVERT: E 243 MET cc_start: 0.7427 (tpp) cc_final: 0.7106 (tpp) REVERT: E 244 HIS cc_start: 0.8418 (m170) cc_final: 0.8196 (m-70) REVERT: E 247 MET cc_start: 0.8129 (mmm) cc_final: 0.7457 (tmm) REVERT: E 254 CYS cc_start: 0.8503 (t) cc_final: 0.8189 (p) REVERT: E 258 TRP cc_start: 0.8060 (m100) cc_final: 0.7195 (m100) REVERT: E 310 LEU cc_start: 0.7492 (mt) cc_final: 0.7199 (mt) REVERT: B 66 MET cc_start: 0.7812 (mmm) cc_final: 0.7486 (tpt) REVERT: B 87 GLU cc_start: 0.8313 (tp30) cc_final: 0.7660 (tp30) REVERT: B 212 SER cc_start: 0.9063 (m) cc_final: 0.8585 (p) REVERT: B 422 MET cc_start: 0.7658 (ttm) cc_final: 0.7365 (ttt) REVERT: B 711 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7826 (tp40) REVERT: C 66 MET cc_start: 0.7810 (mmm) cc_final: 0.7480 (tpt) REVERT: C 87 GLU cc_start: 0.8314 (tp30) cc_final: 0.7662 (tp30) REVERT: C 212 SER cc_start: 0.9060 (m) cc_final: 0.8586 (p) REVERT: C 422 MET cc_start: 0.7658 (ttm) cc_final: 0.7367 (ttt) REVERT: C 711 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7829 (tp40) REVERT: D 66 MET cc_start: 0.7819 (mmm) cc_final: 0.7492 (tpt) REVERT: D 87 GLU cc_start: 0.8316 (tp30) cc_final: 0.7664 (tp30) REVERT: D 212 SER cc_start: 0.9060 (m) cc_final: 0.8585 (p) REVERT: D 422 MET cc_start: 0.7657 (ttm) cc_final: 0.7368 (ttt) REVERT: D 711 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7834 (tp40) REVERT: F 240 MET cc_start: 0.7858 (tpt) cc_final: 0.7586 (tpt) REVERT: F 243 MET cc_start: 0.7404 (tpp) cc_final: 0.7070 (tpp) REVERT: F 244 HIS cc_start: 0.8424 (m170) cc_final: 0.8213 (m-70) REVERT: F 247 MET cc_start: 0.8133 (mmm) cc_final: 0.7499 (tmm) REVERT: F 254 CYS cc_start: 0.8517 (t) cc_final: 0.8089 (p) REVERT: F 258 TRP cc_start: 0.8033 (m100) cc_final: 0.7130 (m100) REVERT: F 310 LEU cc_start: 0.7512 (mt) cc_final: 0.6985 (mt) REVERT: G 240 MET cc_start: 0.7871 (tpt) cc_final: 0.7598 (tpt) REVERT: G 243 MET cc_start: 0.7419 (tpp) cc_final: 0.7094 (tpp) REVERT: G 247 MET cc_start: 0.8136 (mmm) cc_final: 0.7499 (tmm) REVERT: G 254 CYS cc_start: 0.8520 (t) cc_final: 0.8081 (p) REVERT: G 258 TRP cc_start: 0.8040 (m100) cc_final: 0.7133 (m100) REVERT: G 310 LEU cc_start: 0.7503 (mt) cc_final: 0.6980 (mt) REVERT: H 240 MET cc_start: 0.7852 (tpt) cc_final: 0.7584 (tpt) REVERT: H 243 MET cc_start: 0.7406 (tpp) cc_final: 0.7072 (tpp) REVERT: H 247 MET cc_start: 0.8138 (mmm) cc_final: 0.7500 (tmm) REVERT: H 254 CYS cc_start: 0.8527 (t) cc_final: 0.8088 (p) REVERT: H 258 TRP cc_start: 0.8048 (m100) cc_final: 0.7151 (m100) REVERT: H 310 LEU cc_start: 0.7496 (mt) cc_final: 0.6974 (mt) outliers start: 52 outliers final: 33 residues processed: 445 average time/residue: 0.4540 time to fit residues: 322.8224 Evaluate side-chains 370 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 337 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 286 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33576 Z= 0.226 Angle : 0.528 9.177 45420 Z= 0.273 Chirality : 0.039 0.137 5080 Planarity : 0.003 0.035 5652 Dihedral : 11.867 179.083 4908 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 10.46 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.14), residues: 3928 helix: 1.73 (0.10), residues: 2564 sheet: -1.08 (0.39), residues: 160 loop : -0.35 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 327 HIS 0.008 0.001 HIS A 326 PHE 0.021 0.001 PHE F 189 TYR 0.018 0.001 TYR A 524 ARG 0.002 0.000 ARG E 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 370 time to evaluate : 3.607 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.8025 (mmm) cc_final: 0.7678 (tpt) REVERT: A 87 GLU cc_start: 0.8172 (tp30) cc_final: 0.7464 (tp30) REVERT: A 212 SER cc_start: 0.9006 (m) cc_final: 0.8541 (p) REVERT: A 422 MET cc_start: 0.7588 (ttm) cc_final: 0.7300 (ttt) REVERT: A 711 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7687 (tp-100) REVERT: E 38 LEU cc_start: 0.8278 (mp) cc_final: 0.7970 (mt) REVERT: E 178 ARG cc_start: 0.6940 (tpt170) cc_final: 0.6680 (tpt90) REVERT: E 209 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8893 (mmmm) REVERT: E 240 MET cc_start: 0.7835 (tpt) cc_final: 0.7542 (tpt) REVERT: E 247 MET cc_start: 0.8205 (mmm) cc_final: 0.7352 (tmm) REVERT: E 254 CYS cc_start: 0.8479 (t) cc_final: 0.8079 (p) REVERT: E 258 TRP cc_start: 0.8183 (m100) cc_final: 0.7520 (m100) REVERT: E 310 LEU cc_start: 0.7380 (mt) cc_final: 0.6904 (mt) REVERT: B 66 MET cc_start: 0.7934 (mmm) cc_final: 0.7618 (tpt) REVERT: B 87 GLU cc_start: 0.8180 (tp30) cc_final: 0.7463 (tp30) REVERT: B 212 SER cc_start: 0.9011 (m) cc_final: 0.8546 (p) REVERT: B 422 MET cc_start: 0.7595 (ttm) cc_final: 0.7302 (ttt) REVERT: B 711 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7686 (tp-100) REVERT: C 66 MET cc_start: 0.7928 (mmm) cc_final: 0.7613 (tpt) REVERT: C 87 GLU cc_start: 0.8181 (tp30) cc_final: 0.7468 (tp30) REVERT: C 212 SER cc_start: 0.9008 (m) cc_final: 0.8542 (p) REVERT: C 422 MET cc_start: 0.7591 (ttm) cc_final: 0.7299 (ttt) REVERT: C 711 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7691 (tp-100) REVERT: D 66 MET cc_start: 0.8002 (mmm) cc_final: 0.7670 (tpt) REVERT: D 87 GLU cc_start: 0.8228 (tp30) cc_final: 0.7499 (tp30) REVERT: D 212 SER cc_start: 0.9009 (m) cc_final: 0.8547 (p) REVERT: D 422 MET cc_start: 0.7594 (ttm) cc_final: 0.7303 (ttt) REVERT: D 619 MET cc_start: 0.7668 (ttm) cc_final: 0.7448 (ttm) REVERT: D 711 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7691 (tp-100) REVERT: F 178 ARG cc_start: 0.6876 (tpt170) cc_final: 0.6522 (tpt90) REVERT: F 240 MET cc_start: 0.7878 (tpt) cc_final: 0.7602 (tpt) REVERT: F 247 MET cc_start: 0.8200 (mmm) cc_final: 0.7363 (tmm) REVERT: F 254 CYS cc_start: 0.8484 (t) cc_final: 0.8078 (p) REVERT: F 258 TRP cc_start: 0.8154 (m100) cc_final: 0.7535 (m100) REVERT: F 310 LEU cc_start: 0.7393 (mt) cc_final: 0.6907 (mt) REVERT: G 178 ARG cc_start: 0.6868 (tpt170) cc_final: 0.6510 (tpt90) REVERT: G 240 MET cc_start: 0.7937 (tpt) cc_final: 0.7671 (tpt) REVERT: G 243 MET cc_start: 0.7380 (tpp) cc_final: 0.7166 (tpp) REVERT: G 247 MET cc_start: 0.8211 (mmm) cc_final: 0.7364 (tmm) REVERT: G 254 CYS cc_start: 0.8478 (t) cc_final: 0.8073 (p) REVERT: G 258 TRP cc_start: 0.8182 (m100) cc_final: 0.7580 (m100) REVERT: G 310 LEU cc_start: 0.7375 (mt) cc_final: 0.6894 (mt) REVERT: H 178 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6514 (tpt90) REVERT: H 240 MET cc_start: 0.7920 (tpt) cc_final: 0.7653 (tpt) REVERT: H 243 MET cc_start: 0.7406 (tpp) cc_final: 0.7193 (tpp) REVERT: H 247 MET cc_start: 0.8208 (mmm) cc_final: 0.7367 (tmm) REVERT: H 254 CYS cc_start: 0.8487 (t) cc_final: 0.8076 (p) REVERT: H 258 TRP cc_start: 0.8157 (m100) cc_final: 0.7542 (m100) REVERT: H 310 LEU cc_start: 0.7376 (mt) cc_final: 0.6896 (mt) outliers start: 52 outliers final: 33 residues processed: 395 average time/residue: 0.4266 time to fit residues: 281.3223 Evaluate side-chains 371 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 338 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33576 Z= 0.388 Angle : 0.627 9.975 45420 Z= 0.316 Chirality : 0.042 0.213 5080 Planarity : 0.004 0.033 5652 Dihedral : 11.040 140.465 4908 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 10.91 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.14), residues: 3928 helix: 1.69 (0.10), residues: 2580 sheet: -1.11 (0.39), residues: 160 loop : -0.35 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 315 HIS 0.013 0.001 HIS A 326 PHE 0.019 0.002 PHE D 319 TYR 0.021 0.002 TYR A 524 ARG 0.003 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 348 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8052 (mmm) cc_final: 0.7592 (tpt) REVERT: A 87 GLU cc_start: 0.8202 (tp30) cc_final: 0.7483 (tp30) REVERT: A 212 SER cc_start: 0.9094 (m) cc_final: 0.8727 (p) REVERT: A 422 MET cc_start: 0.7695 (ttm) cc_final: 0.7405 (ttt) REVERT: A 711 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7734 (tp40) REVERT: E 195 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.3629 (m-10) REVERT: E 247 MET cc_start: 0.8279 (mmm) cc_final: 0.7435 (tmm) REVERT: E 254 CYS cc_start: 0.8502 (t) cc_final: 0.8199 (p) REVERT: E 258 TRP cc_start: 0.8408 (m100) cc_final: 0.7853 (m100) REVERT: E 310 LEU cc_start: 0.7557 (mt) cc_final: 0.7160 (mt) REVERT: B 66 MET cc_start: 0.8061 (mmm) cc_final: 0.7699 (tpt) REVERT: B 87 GLU cc_start: 0.8208 (tp30) cc_final: 0.7486 (tp30) REVERT: B 212 SER cc_start: 0.9096 (m) cc_final: 0.8726 (p) REVERT: B 422 MET cc_start: 0.7698 (ttm) cc_final: 0.7407 (ttt) REVERT: B 711 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7731 (tp40) REVERT: C 66 MET cc_start: 0.8060 (mmm) cc_final: 0.7688 (tpt) REVERT: C 212 SER cc_start: 0.9092 (m) cc_final: 0.8725 (p) REVERT: C 422 MET cc_start: 0.7698 (ttm) cc_final: 0.7406 (ttt) REVERT: C 711 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7733 (tp40) REVERT: D 66 MET cc_start: 0.8034 (mmm) cc_final: 0.7601 (tpt) REVERT: D 212 SER cc_start: 0.9091 (m) cc_final: 0.8720 (p) REVERT: D 422 MET cc_start: 0.7700 (ttm) cc_final: 0.7404 (ttt) REVERT: D 711 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7736 (tp40) REVERT: F 195 TYR cc_start: 0.5962 (OUTLIER) cc_final: 0.3513 (m-10) REVERT: F 240 MET cc_start: 0.7965 (tpt) cc_final: 0.7762 (tpt) REVERT: F 247 MET cc_start: 0.8241 (mmm) cc_final: 0.7410 (tmm) REVERT: F 254 CYS cc_start: 0.8507 (t) cc_final: 0.8184 (p) REVERT: F 258 TRP cc_start: 0.8380 (m100) cc_final: 0.7796 (m100) REVERT: F 310 LEU cc_start: 0.7568 (mt) cc_final: 0.7152 (mt) REVERT: G 195 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.3523 (m-10) REVERT: G 243 MET cc_start: 0.7504 (tpp) cc_final: 0.7279 (tpp) REVERT: G 247 MET cc_start: 0.8270 (mmm) cc_final: 0.7413 (tmm) REVERT: G 254 CYS cc_start: 0.8505 (t) cc_final: 0.8183 (p) REVERT: G 258 TRP cc_start: 0.8403 (m100) cc_final: 0.7806 (m100) REVERT: G 310 LEU cc_start: 0.7549 (mt) cc_final: 0.7150 (mt) REVERT: H 195 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.3509 (m-10) REVERT: H 247 MET cc_start: 0.8269 (mmm) cc_final: 0.7414 (tmm) REVERT: H 254 CYS cc_start: 0.8514 (t) cc_final: 0.8181 (p) REVERT: H 258 TRP cc_start: 0.8388 (m100) cc_final: 0.7790 (m100) REVERT: H 310 LEU cc_start: 0.7543 (mt) cc_final: 0.7134 (mt) outliers start: 87 outliers final: 65 residues processed: 388 average time/residue: 0.4422 time to fit residues: 287.0233 Evaluate side-chains 399 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain H residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 340 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS H 244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33576 Z= 0.160 Angle : 0.494 7.734 45420 Z= 0.253 Chirality : 0.038 0.164 5080 Planarity : 0.003 0.034 5652 Dihedral : 10.349 141.138 4908 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.75 % Allowed : 12.88 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.14), residues: 3928 helix: 1.97 (0.10), residues: 2584 sheet: -0.96 (0.40), residues: 160 loop : -0.16 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 327 HIS 0.009 0.001 HIS A 326 PHE 0.021 0.001 PHE E 336 TYR 0.017 0.001 TYR B 524 ARG 0.003 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 348 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6972 (tt) REVERT: A 212 SER cc_start: 0.9044 (m) cc_final: 0.8680 (p) REVERT: A 422 MET cc_start: 0.7615 (ttm) cc_final: 0.7348 (ttt) REVERT: A 619 MET cc_start: 0.7521 (ttm) cc_final: 0.7312 (ttm) REVERT: E 38 LEU cc_start: 0.8275 (mp) cc_final: 0.8029 (mt) REVERT: E 195 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.3590 (m-10) REVERT: E 244 HIS cc_start: 0.8281 (m170) cc_final: 0.8020 (m-70) REVERT: E 247 MET cc_start: 0.8279 (mmm) cc_final: 0.7383 (tmm) REVERT: E 254 CYS cc_start: 0.8524 (t) cc_final: 0.8157 (p) REVERT: E 258 TRP cc_start: 0.8395 (m100) cc_final: 0.7857 (m100) REVERT: E 310 LEU cc_start: 0.7434 (mt) cc_final: 0.6992 (mt) REVERT: B 69 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6951 (tt) REVERT: B 212 SER cc_start: 0.9040 (m) cc_final: 0.8678 (p) REVERT: B 422 MET cc_start: 0.7619 (ttm) cc_final: 0.7354 (ttt) REVERT: B 619 MET cc_start: 0.7530 (ttm) cc_final: 0.7300 (ttm) REVERT: C 69 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6960 (tt) REVERT: C 212 SER cc_start: 0.9042 (m) cc_final: 0.8681 (p) REVERT: C 422 MET cc_start: 0.7620 (ttm) cc_final: 0.7353 (ttt) REVERT: C 619 MET cc_start: 0.7533 (ttm) cc_final: 0.7311 (ttm) REVERT: D 69 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6997 (tt) REVERT: D 212 SER cc_start: 0.9034 (m) cc_final: 0.8673 (p) REVERT: D 422 MET cc_start: 0.7614 (ttm) cc_final: 0.7351 (ttt) REVERT: F 195 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.3427 (m-10) REVERT: F 244 HIS cc_start: 0.8268 (m170) cc_final: 0.8000 (m-70) REVERT: F 247 MET cc_start: 0.8278 (mmm) cc_final: 0.7395 (tmm) REVERT: F 254 CYS cc_start: 0.8504 (t) cc_final: 0.8142 (p) REVERT: F 258 TRP cc_start: 0.8409 (m100) cc_final: 0.7782 (m100) REVERT: F 310 LEU cc_start: 0.7442 (mt) cc_final: 0.6960 (mt) REVERT: G 195 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.3475 (m-10) REVERT: G 243 MET cc_start: 0.7415 (tpp) cc_final: 0.6856 (tpp) REVERT: G 247 MET cc_start: 0.8297 (mmm) cc_final: 0.7360 (tmm) REVERT: G 254 CYS cc_start: 0.8521 (t) cc_final: 0.8151 (p) REVERT: G 258 TRP cc_start: 0.8400 (m100) cc_final: 0.7773 (m100) REVERT: G 310 LEU cc_start: 0.7411 (mt) cc_final: 0.6936 (mt) REVERT: H 195 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.3424 (m-10) REVERT: H 247 MET cc_start: 0.8308 (mmm) cc_final: 0.7404 (tmm) REVERT: H 254 CYS cc_start: 0.8514 (t) cc_final: 0.8146 (p) REVERT: H 258 TRP cc_start: 0.8418 (m100) cc_final: 0.7813 (m100) REVERT: H 310 LEU cc_start: 0.7395 (mt) cc_final: 0.6928 (mt) outliers start: 62 outliers final: 52 residues processed: 377 average time/residue: 0.4084 time to fit residues: 258.2995 Evaluate side-chains 392 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 332 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 379 optimal weight: 7.9990 chunk 314 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 33576 Z= 0.384 Angle : 0.594 7.378 45420 Z= 0.300 Chirality : 0.041 0.155 5080 Planarity : 0.003 0.033 5652 Dihedral : 10.744 142.555 4908 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.31 % Allowed : 13.50 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.14), residues: 3928 helix: 1.90 (0.10), residues: 2584 sheet: -1.09 (0.40), residues: 160 loop : -0.21 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 315 HIS 0.008 0.001 HIS A 326 PHE 0.017 0.002 PHE A 531 TYR 0.020 0.001 TYR B 524 ARG 0.003 0.000 ARG H 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 331 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7735 (tpt) REVERT: A 130 LEU cc_start: 0.8444 (tp) cc_final: 0.8202 (tp) REVERT: A 212 SER cc_start: 0.9095 (m) cc_final: 0.8755 (p) REVERT: A 422 MET cc_start: 0.7689 (ttm) cc_final: 0.7391 (ttt) REVERT: A 711 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7718 (tp40) REVERT: E 195 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.3744 (m-10) REVERT: E 247 MET cc_start: 0.8347 (mmm) cc_final: 0.7512 (tmm) REVERT: E 254 CYS cc_start: 0.8488 (t) cc_final: 0.8083 (p) REVERT: E 258 TRP cc_start: 0.8639 (m100) cc_final: 0.7941 (m100) REVERT: E 310 LEU cc_start: 0.7735 (mt) cc_final: 0.7277 (mt) REVERT: B 66 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7778 (tpt) REVERT: B 130 LEU cc_start: 0.8439 (tp) cc_final: 0.8204 (tp) REVERT: B 212 SER cc_start: 0.9091 (m) cc_final: 0.8751 (p) REVERT: B 422 MET cc_start: 0.7687 (ttm) cc_final: 0.7392 (ttt) REVERT: B 624 MET cc_start: 0.7595 (mtm) cc_final: 0.7341 (mtm) REVERT: B 711 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7716 (tp40) REVERT: C 66 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (tpt) REVERT: C 130 LEU cc_start: 0.8429 (tp) cc_final: 0.8192 (tp) REVERT: C 212 SER cc_start: 0.9090 (m) cc_final: 0.8753 (p) REVERT: C 422 MET cc_start: 0.7688 (ttm) cc_final: 0.7391 (ttt) REVERT: C 624 MET cc_start: 0.7583 (mtm) cc_final: 0.7326 (mtm) REVERT: C 711 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7722 (tp40) REVERT: D 66 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7749 (tpt) REVERT: D 130 LEU cc_start: 0.8434 (tp) cc_final: 0.8202 (tp) REVERT: D 212 SER cc_start: 0.9089 (m) cc_final: 0.8751 (p) REVERT: D 422 MET cc_start: 0.7683 (ttm) cc_final: 0.7392 (ttt) REVERT: D 624 MET cc_start: 0.7581 (mtm) cc_final: 0.7331 (mtm) REVERT: D 711 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7720 (tp40) REVERT: F 195 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.3585 (m-10) REVERT: F 247 MET cc_start: 0.8349 (mmm) cc_final: 0.7510 (tmm) REVERT: F 254 CYS cc_start: 0.8471 (t) cc_final: 0.8076 (p) REVERT: F 258 TRP cc_start: 0.8636 (m100) cc_final: 0.7933 (m100) REVERT: F 310 LEU cc_start: 0.7718 (mt) cc_final: 0.7266 (mt) REVERT: G 195 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.3459 (m-10) REVERT: G 247 MET cc_start: 0.8361 (mmm) cc_final: 0.7449 (tmm) REVERT: G 254 CYS cc_start: 0.8489 (t) cc_final: 0.8083 (p) REVERT: G 258 TRP cc_start: 0.8633 (m100) cc_final: 0.7915 (m100) REVERT: G 310 LEU cc_start: 0.7561 (mt) cc_final: 0.7114 (mt) REVERT: H 195 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.3631 (m-10) REVERT: H 247 MET cc_start: 0.8340 (mmm) cc_final: 0.7473 (tmm) REVERT: H 254 CYS cc_start: 0.8479 (t) cc_final: 0.8079 (p) REVERT: H 258 TRP cc_start: 0.8639 (m100) cc_final: 0.7941 (m100) REVERT: H 310 LEU cc_start: 0.7677 (mt) cc_final: 0.7225 (mt) outliers start: 82 outliers final: 64 residues processed: 369 average time/residue: 0.4132 time to fit residues: 254.5007 Evaluate side-chains 399 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 327 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 276 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 ASN ** G 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33576 Z= 0.152 Angle : 0.498 7.614 45420 Z= 0.252 Chirality : 0.037 0.148 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.322 142.446 4908 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.09 % Allowed : 14.57 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.14), residues: 3928 helix: 2.07 (0.10), residues: 2580 sheet: -0.91 (0.42), residues: 160 loop : -0.09 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 327 HIS 0.007 0.001 HIS A 326 PHE 0.014 0.001 PHE B 540 TYR 0.017 0.001 TYR A 524 ARG 0.002 0.000 ARG H 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 332 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7752 (tpt) REVERT: A 69 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6983 (tt) REVERT: A 212 SER cc_start: 0.9077 (m) cc_final: 0.8747 (p) REVERT: A 422 MET cc_start: 0.7598 (ttm) cc_final: 0.7339 (ttt) REVERT: E 195 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.3646 (m-10) REVERT: E 247 MET cc_start: 0.8254 (mmm) cc_final: 0.7384 (tmm) REVERT: E 254 CYS cc_start: 0.8380 (t) cc_final: 0.7961 (p) REVERT: E 258 TRP cc_start: 0.8595 (m100) cc_final: 0.7783 (m100) REVERT: E 310 LEU cc_start: 0.7593 (mt) cc_final: 0.7102 (mt) REVERT: B 66 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7774 (tpt) REVERT: B 69 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6964 (tt) REVERT: B 212 SER cc_start: 0.9072 (m) cc_final: 0.8745 (p) REVERT: B 422 MET cc_start: 0.7602 (ttm) cc_final: 0.7362 (ttt) REVERT: C 66 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7756 (tpt) REVERT: C 69 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6968 (tt) REVERT: C 212 SER cc_start: 0.9074 (m) cc_final: 0.8747 (p) REVERT: C 422 MET cc_start: 0.7603 (ttm) cc_final: 0.7344 (ttt) REVERT: D 66 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7766 (tpt) REVERT: D 69 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6977 (tt) REVERT: D 212 SER cc_start: 0.9069 (m) cc_final: 0.8741 (p) REVERT: D 422 MET cc_start: 0.7599 (ttm) cc_final: 0.7347 (ttt) REVERT: F 195 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.3382 (m-10) REVERT: F 247 MET cc_start: 0.8250 (mmm) cc_final: 0.7391 (tmm) REVERT: F 254 CYS cc_start: 0.8357 (t) cc_final: 0.7947 (p) REVERT: F 258 TRP cc_start: 0.8587 (m100) cc_final: 0.7905 (m100) REVERT: F 310 LEU cc_start: 0.7572 (mt) cc_final: 0.7101 (mt) REVERT: G 195 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.3520 (m-10) REVERT: G 247 MET cc_start: 0.8340 (mmm) cc_final: 0.7395 (tmm) REVERT: G 254 CYS cc_start: 0.8378 (t) cc_final: 0.7936 (p) REVERT: G 258 TRP cc_start: 0.8556 (m100) cc_final: 0.7745 (m100) REVERT: G 310 LEU cc_start: 0.7604 (mt) cc_final: 0.7097 (mt) REVERT: H 195 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.3379 (m-10) REVERT: H 247 MET cc_start: 0.8279 (mmm) cc_final: 0.7396 (tmm) REVERT: H 254 CYS cc_start: 0.8368 (t) cc_final: 0.7957 (p) REVERT: H 258 TRP cc_start: 0.8587 (m100) cc_final: 0.7791 (m100) REVERT: H 310 LEU cc_start: 0.7546 (mt) cc_final: 0.7078 (mt) outliers start: 74 outliers final: 58 residues processed: 368 average time/residue: 0.4116 time to fit residues: 252.0943 Evaluate side-chains 395 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 325 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 296 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33576 Z= 0.185 Angle : 0.513 11.234 45420 Z= 0.257 Chirality : 0.038 0.198 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.196 142.937 4908 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.06 % Allowed : 14.74 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.14), residues: 3928 helix: 2.11 (0.10), residues: 2584 sheet: -0.79 (0.42), residues: 160 loop : -0.11 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 315 HIS 0.008 0.001 HIS A 326 PHE 0.014 0.001 PHE B 540 TYR 0.018 0.001 TYR C 524 ARG 0.002 0.000 ARG G 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 350 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7740 (tpt) REVERT: A 212 SER cc_start: 0.9039 (m) cc_final: 0.8692 (p) REVERT: A 422 MET cc_start: 0.7628 (ttm) cc_final: 0.7352 (ttt) REVERT: A 711 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7634 (tp40) REVERT: E 195 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.3700 (m-10) REVERT: E 247 MET cc_start: 0.8248 (mmm) cc_final: 0.7384 (tmm) REVERT: E 254 CYS cc_start: 0.8355 (t) cc_final: 0.7905 (p) REVERT: E 258 TRP cc_start: 0.8583 (m100) cc_final: 0.7812 (m100) REVERT: E 310 LEU cc_start: 0.7540 (mt) cc_final: 0.7055 (mt) REVERT: B 66 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7753 (tpt) REVERT: B 120 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7611 (ppt170) REVERT: B 212 SER cc_start: 0.9035 (m) cc_final: 0.8690 (p) REVERT: B 422 MET cc_start: 0.7632 (ttm) cc_final: 0.7363 (ttt) REVERT: B 711 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7632 (tp40) REVERT: C 66 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7742 (tpt) REVERT: C 120 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7620 (ppt170) REVERT: C 212 SER cc_start: 0.9035 (m) cc_final: 0.8688 (p) REVERT: C 422 MET cc_start: 0.7618 (ttm) cc_final: 0.7366 (ttt) REVERT: C 711 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7641 (tp40) REVERT: D 66 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7754 (tpt) REVERT: D 69 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7002 (tt) REVERT: D 212 SER cc_start: 0.9030 (m) cc_final: 0.8684 (p) REVERT: D 422 MET cc_start: 0.7615 (ttm) cc_final: 0.7360 (ttt) REVERT: D 711 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7637 (tp40) REVERT: F 195 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.3345 (m-10) REVERT: F 247 MET cc_start: 0.8240 (mmm) cc_final: 0.7349 (tmm) REVERT: F 254 CYS cc_start: 0.8348 (t) cc_final: 0.7922 (p) REVERT: F 258 TRP cc_start: 0.8576 (m100) cc_final: 0.7844 (m100) REVERT: F 310 LEU cc_start: 0.7584 (mt) cc_final: 0.7071 (mt) REVERT: G 195 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.3523 (m-10) REVERT: G 247 MET cc_start: 0.8254 (mmm) cc_final: 0.7345 (tmm) REVERT: G 254 CYS cc_start: 0.8359 (t) cc_final: 0.7920 (p) REVERT: G 258 TRP cc_start: 0.8582 (m100) cc_final: 0.7820 (m100) REVERT: G 310 LEU cc_start: 0.7565 (mt) cc_final: 0.7080 (mt) REVERT: H 195 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.3347 (m-10) REVERT: H 247 MET cc_start: 0.8287 (mmm) cc_final: 0.7397 (tmm) REVERT: H 254 CYS cc_start: 0.8355 (t) cc_final: 0.7920 (p) REVERT: H 258 TRP cc_start: 0.8573 (m100) cc_final: 0.7848 (m100) REVERT: H 310 LEU cc_start: 0.7544 (mt) cc_final: 0.7067 (mt) outliers start: 73 outliers final: 51 residues processed: 383 average time/residue: 0.4368 time to fit residues: 286.4344 Evaluate side-chains 401 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 339 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 0.4980 chunk 332 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 244 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33576 Z= 0.370 Angle : 0.595 8.262 45420 Z= 0.300 Chirality : 0.041 0.206 5080 Planarity : 0.003 0.033 5652 Dihedral : 10.547 144.795 4908 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.62 % Allowed : 14.52 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.14), residues: 3928 helix: 1.99 (0.10), residues: 2584 sheet: -0.83 (0.40), residues: 160 loop : -0.11 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 211 HIS 0.008 0.001 HIS A 326 PHE 0.017 0.002 PHE C 540 TYR 0.019 0.001 TYR A 524 ARG 0.002 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 340 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7789 (tpt) REVERT: A 212 SER cc_start: 0.9139 (m) cc_final: 0.8786 (p) REVERT: A 422 MET cc_start: 0.7729 (ttm) cc_final: 0.7422 (ttt) REVERT: A 624 MET cc_start: 0.7896 (ptp) cc_final: 0.7430 (mtm) REVERT: A 711 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7668 (tp40) REVERT: E 195 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.3713 (m-10) REVERT: E 247 MET cc_start: 0.8342 (mmm) cc_final: 0.7488 (tmm) REVERT: E 254 CYS cc_start: 0.8333 (t) cc_final: 0.7877 (p) REVERT: E 258 TRP cc_start: 0.8670 (m100) cc_final: 0.7912 (m100) REVERT: E 310 LEU cc_start: 0.7693 (mt) cc_final: 0.7208 (mt) REVERT: B 66 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7807 (tpt) REVERT: B 120 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7743 (ppt170) REVERT: B 212 SER cc_start: 0.9132 (m) cc_final: 0.8784 (p) REVERT: B 422 MET cc_start: 0.7730 (ttm) cc_final: 0.7417 (ttt) REVERT: B 711 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7662 (tp40) REVERT: C 66 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7792 (tpt) REVERT: C 120 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7741 (ppt170) REVERT: C 212 SER cc_start: 0.9134 (m) cc_final: 0.8781 (p) REVERT: C 422 MET cc_start: 0.7739 (ttm) cc_final: 0.7418 (ttt) REVERT: C 711 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7667 (tp40) REVERT: D 66 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7793 (tpt) REVERT: D 87 GLU cc_start: 0.8183 (tp30) cc_final: 0.7306 (tp30) REVERT: D 212 SER cc_start: 0.9128 (m) cc_final: 0.8780 (p) REVERT: D 422 MET cc_start: 0.7727 (ttm) cc_final: 0.7415 (ttt) REVERT: D 711 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7666 (tp40) REVERT: F 195 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.3613 (m-10) REVERT: F 247 MET cc_start: 0.8306 (mmm) cc_final: 0.7463 (tmm) REVERT: F 254 CYS cc_start: 0.8325 (t) cc_final: 0.7905 (p) REVERT: F 258 TRP cc_start: 0.8667 (m100) cc_final: 0.7918 (m100) REVERT: F 310 LEU cc_start: 0.7760 (mt) cc_final: 0.7253 (mt) REVERT: G 195 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.3708 (m-10) REVERT: G 247 MET cc_start: 0.8386 (mmm) cc_final: 0.7498 (tmm) REVERT: G 254 CYS cc_start: 0.8291 (t) cc_final: 0.7833 (p) REVERT: G 258 TRP cc_start: 0.8661 (m100) cc_final: 0.7905 (m100) REVERT: G 310 LEU cc_start: 0.7699 (mt) cc_final: 0.7216 (mt) REVERT: H 195 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.3613 (m-10) REVERT: H 247 MET cc_start: 0.8342 (mmm) cc_final: 0.7468 (tmm) REVERT: H 254 CYS cc_start: 0.8286 (t) cc_final: 0.7824 (p) REVERT: H 258 TRP cc_start: 0.8678 (m100) cc_final: 0.7923 (m100) REVERT: H 310 LEU cc_start: 0.7671 (mt) cc_final: 0.7192 (mt) outliers start: 93 outliers final: 77 residues processed: 384 average time/residue: 0.4269 time to fit residues: 276.5291 Evaluate side-chains 422 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 335 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 195 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.8980 chunk 372 optimal weight: 9.9990 chunk 227 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 390 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33576 Z= 0.157 Angle : 0.516 9.821 45420 Z= 0.259 Chirality : 0.038 0.207 5080 Planarity : 0.003 0.031 5652 Dihedral : 10.128 144.641 4908 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 15.39 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.14), residues: 3928 helix: 2.11 (0.10), residues: 2584 sheet: -0.76 (0.42), residues: 160 loop : -0.08 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 211 HIS 0.008 0.001 HIS A 326 PHE 0.013 0.001 PHE G 189 TYR 0.019 0.001 TYR C 524 ARG 0.002 0.000 ARG H 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 339 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7700 (tpt) REVERT: A 130 LEU cc_start: 0.8454 (tp) cc_final: 0.8064 (tt) REVERT: A 212 SER cc_start: 0.9066 (m) cc_final: 0.8726 (p) REVERT: A 422 MET cc_start: 0.7616 (ttm) cc_final: 0.7359 (ttt) REVERT: E 195 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.3700 (m-10) REVERT: E 247 MET cc_start: 0.8243 (mmm) cc_final: 0.7337 (tmm) REVERT: E 254 CYS cc_start: 0.8322 (t) cc_final: 0.7928 (p) REVERT: E 258 TRP cc_start: 0.8647 (m100) cc_final: 0.7873 (m100) REVERT: E 310 LEU cc_start: 0.7607 (mt) cc_final: 0.7051 (mt) REVERT: B 66 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7714 (tpt) REVERT: B 120 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7761 (ppt170) REVERT: B 130 LEU cc_start: 0.8470 (tp) cc_final: 0.8097 (tt) REVERT: B 212 SER cc_start: 0.9059 (m) cc_final: 0.8724 (p) REVERT: B 422 MET cc_start: 0.7604 (ttm) cc_final: 0.7349 (ttt) REVERT: C 66 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7702 (tpt) REVERT: C 120 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7761 (ppt170) REVERT: C 212 SER cc_start: 0.9062 (m) cc_final: 0.8721 (p) REVERT: C 422 MET cc_start: 0.7614 (ttm) cc_final: 0.7358 (ttt) REVERT: D 66 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (tpt) REVERT: D 69 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6992 (tt) REVERT: D 130 LEU cc_start: 0.8445 (tp) cc_final: 0.8068 (tt) REVERT: D 212 SER cc_start: 0.9055 (m) cc_final: 0.8725 (p) REVERT: D 422 MET cc_start: 0.7610 (ttm) cc_final: 0.7355 (ttt) REVERT: F 195 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.3392 (m-10) REVERT: F 247 MET cc_start: 0.8257 (mmm) cc_final: 0.7357 (tmm) REVERT: F 254 CYS cc_start: 0.8271 (t) cc_final: 0.7898 (p) REVERT: F 258 TRP cc_start: 0.8634 (m100) cc_final: 0.7936 (m100) REVERT: F 310 LEU cc_start: 0.7605 (mt) cc_final: 0.7046 (mt) REVERT: G 195 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.3423 (m-10) REVERT: G 247 MET cc_start: 0.8322 (mmm) cc_final: 0.7429 (tmm) REVERT: G 254 CYS cc_start: 0.8286 (t) cc_final: 0.7822 (p) REVERT: G 258 TRP cc_start: 0.8630 (m100) cc_final: 0.7922 (m100) REVERT: G 310 LEU cc_start: 0.7613 (mt) cc_final: 0.7090 (mt) REVERT: H 195 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.3452 (m-10) REVERT: H 247 MET cc_start: 0.8287 (mmm) cc_final: 0.7389 (tmm) REVERT: H 254 CYS cc_start: 0.8307 (t) cc_final: 0.7887 (p) REVERT: H 258 TRP cc_start: 0.8638 (m100) cc_final: 0.7938 (m100) REVERT: H 310 LEU cc_start: 0.7594 (mt) cc_final: 0.7080 (mt) outliers start: 76 outliers final: 60 residues processed: 372 average time/residue: 0.4527 time to fit residues: 284.3347 Evaluate side-chains 407 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 336 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.9990 chunk 331 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 311 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.070935 restraints weight = 75170.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071048 restraints weight = 66507.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.071516 restraints weight = 54157.760| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33576 Z= 0.243 Angle : 0.548 10.627 45420 Z= 0.273 Chirality : 0.039 0.184 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.230 146.553 4908 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.40 % Allowed : 15.16 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.14), residues: 3928 helix: 2.08 (0.10), residues: 2588 sheet: -0.79 (0.41), residues: 160 loop : -0.05 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 211 HIS 0.009 0.001 HIS B 326 PHE 0.015 0.001 PHE C 540 TYR 0.019 0.001 TYR A 524 ARG 0.002 0.000 ARG G 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5976.96 seconds wall clock time: 109 minutes 34.03 seconds (6574.03 seconds total)