Starting phenix.real_space_refine on Sun Feb 18 10:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mit_23864/02_2024/7mit_23864_neut_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 K 4 8.98 5 P 37 5.49 5 S 104 5.16 5 Cl 1 4.86 5 C 13871 2.51 5 N 3594 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "E ARG 590": "NH1" <-> "NH2" Residue "E ARG 774": "NH1" <-> "NH2" Residue "E ARG 804": "NH1" <-> "NH2" Residue "E ARG 815": "NH1" <-> "NH2" Residue "E PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1078": "NH1" <-> "NH2" Residue "E GLU 1173": "OE1" <-> "OE2" Residue "E ARG 1185": "NH1" <-> "NH2" Residue "E ARG 1189": "NH1" <-> "NH2" Residue "E ARG 1193": "NH1" <-> "NH2" Residue "E ARG 1218": "NH1" <-> "NH2" Residue "E ARG 1263": "NH1" <-> "NH2" Residue "E PHE 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21447 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2696 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 12, 'TRANS': 351} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2564 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2546 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 325} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2558 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 9995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1438, 9995 Classifications: {'peptide': 1438} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 47, 'TRANS': 1390} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1828 Unresolved non-hydrogen dihedrals: 1165 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 22, 'TRP:plan': 5, 'ASP:plan': 46, 'PHE:plan': 12, 'GLU:plan': 43, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 817 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 192 Unusual residues: {' K': 3, 'ATP': 1, 'POV': 2, 'PTY': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 152 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 193 Unusual residues: {'ATP': 1, 'POV': 3} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 127 Unusual residues: {' K': 1, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 396 Unusual residues: {'ATP': 1, 'GBM': 1, 'PTY': 7} Classifications: {'peptide': 2, 'undetermined': 9} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 126 Time building chain proxies: 12.06, per 1000 atoms: 0.56 Number of scatterers: 21447 At special positions: 0 Unit cell: (125.54, 168.224, 154.414, 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) K 4 19.00 Cl 1 17.00 S 104 16.00 P 37 15.00 O 3836 8.00 N 3594 7.00 C 13871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 24 " 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 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG N 1 " - " ASN E 9 " Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 4.2 seconds 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 17 sheets defined 46.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 No H-bonds generated for 'chain 'A' and resid 17 through 20' Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.776A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 98 removed outlier: 3.607A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 153 through 182 Processing helix chain 'A' and resid 276 through 279 removed outlier: 4.505A pdb=" N ASP A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 97 removed outlier: 4.014A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 removed outlier: 4.178A pdb=" N GLY B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 153 through 184 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 69 through 97 removed outlier: 4.484A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 153 through 182 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.678A pdb=" N ASP C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.630A pdb=" N LEU D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 97 removed outlier: 4.128A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 153 through 185 removed outlier: 5.743A pdb=" N HIS D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 279 removed outlier: 4.210A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 279' Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'E' and resid 10 through 13 Processing helix chain 'E' and resid 23 through 47 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 70 through 96 removed outlier: 3.580A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 127 Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.552A pdb=" N GLN E 157 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 191 Processing helix chain 'E' and resid 206 through 209 No H-bonds generated for 'chain 'E' and resid 206 through 209' Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 229 through 240 removed outlier: 4.406A pdb=" N THR E 233 " --> pdb=" O TRP E 230 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS E 239 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG E 240 " --> pdb=" O SER E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 277 removed outlier: 3.792A pdb=" N ASP E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 No H-bonds generated for 'chain 'E' and resid 286 through 289' Processing helix chain 'E' and resid 295 through 325 removed outlier: 3.992A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 350 through 393 removed outlier: 3.778A pdb=" N THR E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 415 Processing helix chain 'E' and resid 417 through 431 removed outlier: 3.738A pdb=" N LEU E 427 " --> pdb=" O TRP E 423 " (cutoff:3.500A) Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 434 through 449 Processing helix chain 'E' and resid 452 through 497 removed outlier: 4.022A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Proline residue: E 465 - end of helix Processing helix chain 'E' and resid 500 through 504 Processing helix chain 'E' and resid 510 through 558 removed outlier: 4.248A pdb=" N SER E 514 " --> pdb=" O ILE E 510 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 529 " --> pdb=" O SER E 525 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 3.924A pdb=" N HIS E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 606 removed outlier: 4.242A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR E 580 " --> pdb=" O HIS E 576 " (cutoff:3.500A) Proline residue: E 581 - end of helix removed outlier: 4.408A pdb=" N SER E 586 " --> pdb=" O LEU E 582 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR E 587 " --> pdb=" O PHE E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 715 Processing helix chain 'E' and resid 762 through 767 Processing helix chain 'E' and resid 774 through 784 Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 796 through 798 No H-bonds generated for 'chain 'E' and resid 796 through 798' Processing helix chain 'E' and resid 810 through 822 Processing helix chain 'E' and resid 841 through 854 Processing helix chain 'E' and resid 892 through 897 removed outlier: 4.138A pdb=" N THR E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 909 Processing helix chain 'E' and resid 966 through 971 Processing helix chain 'E' and resid 977 through 984 Processing helix chain 'E' and resid 991 through 1017 removed outlier: 3.784A pdb=" N ASP E1008 " --> pdb=" O ILE E1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 1030 through 1072 removed outlier: 3.750A pdb=" N SER E1050 " --> pdb=" O CYS E1046 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1082 Processing helix chain 'E' and resid 1085 through 1101 Processing helix chain 'E' and resid 1103 through 1127 Processing helix chain 'E' and resid 1129 through 1176 removed outlier: 3.655A pdb=" N ILE E1133 " --> pdb=" O VAL E1130 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E1136 " --> pdb=" O ILE E1133 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 4.916A pdb=" N PHE E1149 " --> pdb=" O GLN E1146 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER E1153 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS E1154 " --> pdb=" O VAL E1151 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP E1161 " --> pdb=" O GLU E1158 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN E1164 " --> pdb=" O ASP E1161 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E1165 " --> pdb=" O SER E1162 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.960A pdb=" N HIS E1170 " --> pdb=" O LEU E1167 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1184 Processing helix chain 'E' and resid 1187 through 1235 removed outlier: 3.877A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1257 removed outlier: 3.873A pdb=" N GLY E1247 " --> pdb=" O LEU E1243 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR E1255 " --> pdb=" O ALA E1251 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1260 through 1283 removed outlier: 4.132A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E1283 " --> pdb=" O ASN E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1295 through 1297 No H-bonds generated for 'chain 'E' and resid 1295 through 1297' Processing helix chain 'E' and resid 1302 through 1304 No H-bonds generated for 'chain 'E' and resid 1302 through 1304' Processing helix chain 'E' and resid 1349 through 1355 Processing helix chain 'E' and resid 1368 through 1370 No H-bonds generated for 'chain 'E' and resid 1368 through 1370' Processing helix chain 'E' and resid 1378 through 1382 Processing helix chain 'E' and resid 1408 through 1413 Processing helix chain 'E' and resid 1417 through 1422 removed outlier: 4.250A pdb=" N GLN E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) Processing helix chain 'E' and resid 1426 through 1429 No H-bonds generated for 'chain 'E' and resid 1426 through 1429' Processing helix chain 'E' and resid 1443 through 1460 removed outlier: 4.556A pdb=" N GLY E1448 " --> pdb=" O ASN E1444 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E1451 " --> pdb=" O VAL E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1476 through 1488 Processing helix chain 'E' and resid 1527 through 1533 Processing helix chain 'E' and resid 1535 through 1540 Processing sheet with id= A, first strand: chain 'A' and resid 191 through 193 Processing sheet with id= B, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.557A pdb=" N GLU A 291 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 322 through 324 Processing sheet with id= D, first strand: chain 'A' and resid 328 through 330 Processing sheet with id= E, first strand: chain 'B' and resid 191 through 193 Processing sheet with id= F, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.769A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 244 through 248 removed outlier: 4.461A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 322 through 324 Processing sheet with id= I, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.584A pdb=" N THR B 329 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 191 through 193 Processing sheet with id= K, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.764A pdb=" N ALA C 197 " --> pdb=" O GLN C 319 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.325A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 291 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= N, first strand: chain 'D' and resid 198 through 202 Processing sheet with id= O, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.365A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU D 291 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D 298 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 322 through 324 Processing sheet with id= Q, first strand: chain 'D' and resid 329 through 331 999 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3271 1.31 - 1.44: 5742 1.44 - 1.57: 12596 1.57 - 1.69: 71 1.69 - 1.82: 163 Bond restraints: 21843 Sorted by residual: bond pdb=" C29 POV D 504 " pdb="C210 POV D 504 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C29 POV D 503 " pdb="C210 POV D 503 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 505 " pdb="C210 POV C 505 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 504 " pdb="C210 POV C 504 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV A 507 " pdb="C210 POV A 507 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 21838 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.48: 376 105.48 - 113.14: 12778 113.14 - 120.79: 9951 120.79 - 128.45: 6419 128.45 - 136.10: 172 Bond angle restraints: 29696 Sorted by residual: angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 121.12 18.75 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.28 18.59 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 122.21 17.66 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP A 504 " pdb=" O3B ATP A 504 " pdb=" PG ATP A 504 " ideal model delta sigma weight residual 139.87 122.45 17.42 1.00e+00 1.00e+00 3.04e+02 ... (remaining 29691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 12707 35.77 - 71.54: 398 71.54 - 107.31: 64 107.31 - 143.08: 12 143.08 - 178.85: 9 Dihedral angle restraints: 13190 sinusoidal: 4994 harmonic: 8196 Sorted by residual: dihedral pdb=" CA ASP E1469 " pdb=" C ASP E1469 " pdb=" N GLU E1470 " pdb=" CA GLU E1470 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" O16 P5S B 504 " pdb=" C2 P5S B 504 " pdb=" C3 P5S B 504 " pdb=" O37 P5S B 504 " ideal model delta sinusoidal sigma weight residual 302.67 123.82 178.85 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O16 P5S E1607 " pdb=" C2 P5S E1607 " pdb=" C3 P5S E1607 " pdb=" O37 P5S E1607 " ideal model delta sinusoidal sigma weight residual 302.67 124.09 178.58 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2739 0.054 - 0.108: 639 0.108 - 0.162: 129 0.162 - 0.216: 7 0.216 - 0.270: 4 Chirality restraints: 3518 Sorted by residual: chirality pdb=" C2 P5S A 508 " pdb=" C1 P5S A 508 " pdb=" C3 P5S A 508 " pdb=" O37 P5S A 508 " both_signs ideal model delta sigma weight residual False 2.32 2.59 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 NAG N 2 " pdb=" C4 NAG N 2 " pdb=" C6 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3515 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 P5S E1607 " -0.366 2.00e-02 2.50e+03 2.11e-01 4.47e+02 pdb=" C20 P5S E1607 " 0.114 2.00e-02 2.50e+03 pdb=" O18 P5S E1607 " 0.124 2.00e-02 2.50e+03 pdb=" O19 P5S E1607 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 P5S A 508 " -0.365 2.00e-02 2.50e+03 2.11e-01 4.43e+02 pdb=" C20 P5S A 508 " 0.112 2.00e-02 2.50e+03 pdb=" O18 P5S A 508 " 0.127 2.00e-02 2.50e+03 pdb=" O19 P5S A 508 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 P5S B 504 " -0.362 2.00e-02 2.50e+03 2.09e-01 4.38e+02 pdb=" C20 P5S B 504 " 0.113 2.00e-02 2.50e+03 pdb=" O18 P5S B 504 " 0.124 2.00e-02 2.50e+03 pdb=" O19 P5S B 504 " 0.126 2.00e-02 2.50e+03 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.67: 385 2.67 - 3.29: 23705 3.29 - 3.91: 38508 3.91 - 4.52: 51400 4.52 - 5.14: 83012 Nonbonded interactions: 197010 Sorted by model distance: nonbonded pdb=" OE1 GLU B 150 " pdb=" OG SER C 129 " model vdw 2.057 2.440 nonbonded pdb=" O TRP E 980 " pdb=" OG SER E 984 " model vdw 2.155 2.440 nonbonded pdb=" OE1 GLU C 150 " pdb=" OG SER D 129 " model vdw 2.155 2.440 nonbonded pdb=" OG SER E 708 " pdb=" OE1 GLN E 753 " model vdw 2.163 2.440 nonbonded pdb=" O LYS E1485 " pdb=" N THR E1489 " model vdw 2.169 2.520 ... (remaining 197005 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 30 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and (n \ ame N or name CA or name C or name O or name CB )) or resid 58 through 64 or (re \ sid 65 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 through 100 or (resid 101 and (name N or name CA or name C o \ r name O or name CB )) or resid 102 through 104 or (resid 105 through 107 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 108 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 27 through 160 or (resid 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 186 or (resid 187 through 189 and (name N or name CA \ or name C or name O or name CB )) or resid 190 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 or (resid 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 242 o \ r (resid 243 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 44 through 246 or (resid 247 through 248 and (name N or name CA or name C or nam \ e O or name CB )) or resid 249 through 261 or (resid 262 through 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 272 or (resid \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throu \ gh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or \ resid 302 or (resid 303 and (name N or name CA or name C or name O or name CB ) \ ) or resid 304 or (resid 305 and (name N or name CA or name C or name O or name \ CB )) or resid 306 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB )) or resid 318 through 358 or (resid 359 through 361 and (na \ me N or name CA or name C or name O or name CB )) or resid 362 through 364 or re \ sid 505)) selection = (chain 'B' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 51 or (resid 52 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 through 100 or (resid 101 and (name N or name CA or name C or name O or \ name CB )) or resid 102 through 104 or (resid 105 through 107 and (name N or nam \ e CA or name C or name O or name CB )) or resid 108 through 149 or (resid 150 an \ d (name N or name CA or name C or name O or name CB )) or resid 151 through 160 \ or (resid 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 186 or (resid 187 through 189 and (name N or name CA or name C or na \ me O or name CB )) or resid 190 through 218 or (resid 219 and (name N or name CA \ or name C or name O or name CB )) or resid 220 through 239 or (resid 240 and (n \ ame N or name CA or name C or name O or name CB )) or resid 241 through 242 or ( \ resid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 \ through 246 or (resid 247 through 248 and (name N or name CA or name C or name O \ or name CB )) or resid 249 through 254 or (resid 255 and (name N or name CA or \ name C or name O or name CB )) or resid 256 through 261 or (resid 262 through 26 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 264 through \ 265 or (resid 266 and (name N or name CA or name C or name O or name CB )) or re \ sid 267 through 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name O \ or name CB )) or resid 276 through 285 or (resid 286 through 287 and (name N or \ name CA or name C or name O or name CB )) or resid 288 or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 through 300 or (resi \ d 301 and (name N or name CA or name C or name O or name CB )) or resid 302 or ( \ resid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 \ through 316 or (resid 317 and (name N or name CA or name C or name O or name CB \ )) or resid 318 through 326 or (resid 327 and (name N or name CA or name C or na \ me O or name CB )) or resid 328 or (resid 329 and (name N or name CA or name C o \ r name O or name CB )) or resid 330 or (resid 331 through 332 and (name N or nam \ e CA or name C or name O or name CB )) or resid 333 through 345 or (resid 346 an \ d (name N or name CA or name C or name O or name CB )) or resid 347 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 or (resid 359 through 361 and (name N or name CA or name C or name O or name \ CB )) or resid 362 through 364 or resid 503)) selection = (chain 'C' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 52 or (resid 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 56 or (res \ id 57 and (name N or name CA or name C or name O or name CB )) or resid 58 or (r \ esid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 thr \ ough 64 or (resid 65 through 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 through 74 or (resid 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 through 116 or (resid 117 through 119 and (nam \ e N or name CA or name C or name O or name CB )) or resid 120 through 125 or (re \ sid 126 and (name N or name CA or name C or name O or name CB )) or resid 127 th \ rough 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 through 188 or (resid 189 and (name N or name CA or name C or name \ O or name CB )) or resid 190 through 216 or (resid 217 and (name N or name CA o \ r name C or name O or name CB )) or resid 218 through 239 or (resid 240 and (nam \ e N or name CA or name C or name O or name CB )) or resid 241 through 242 or (re \ sid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 th \ rough 246 or (resid 247 through 248 and (name N or name CA or name C or name O o \ r name CB )) or resid 249 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB )) or resid 260 through 261 or (resid 262 through 263 \ and (name N or name CA or name C or name O or name CB )) or resid 264 through 26 \ 5 or (resid 266 and (name N or name CA or name C or name O or name CB )) or resi \ d 267 through 274 or (resid 275 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 285 or (resid 286 through 287 and (name N or name \ CA or name C or name O or name CB )) or resid 288 or (resid 289 and (name N or n \ ame CA or name C or name O or name CB )) or resid 290 through 304 or (resid 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 through 31 \ 6 or (resid 317 and (name N or name CA or name C or name O or name CB )) or resi \ d 318 through 326 or (resid 327 and (name N or name CA or name C or name O or na \ me CB )) or resid 328 or (resid 329 and (name N or name CA or name C or name O o \ r name CB )) or resid 330 or (resid 331 through 332 and (name N or name CA or na \ me C or name O or name CB )) or resid 333 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 358 or (resid \ 359 through 361 and (name N or name CA or name C or name O or name CB )) or resi \ d 362 through 364 or resid 504)) selection = (chain 'D' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 51 or (resid 52 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 64 or (resid 65 through 66 and (name N or name CA or name C or name O or name C \ B )) or resid 67 through 74 or (resid 75 and (name N or name CA or name C or nam \ e O or name CB )) or resid 76 through 100 or (resid 101 and (name N or name CA o \ r name C or name O or name CB )) or resid 102 through 104 or (resid 105 through \ 107 and (name N or name CA or name C or name O or name CB )) or (resid 108 throu \ gh 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thr \ ough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 149 or (resid 150 and (name N or name CA or name C or name \ O or name CB )) or resid 151 through 160 or (resid 161 and (name N or name CA or \ name C or name O or name CB )) or resid 162 through 186 or (resid 187 through 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 216 or (resid 217 and (name N or name CA or name C or name O or name CB )) or r \ esid 218 through 239 or (resid 240 and (name N or name CA or name C or name O or \ name CB )) or resid 241 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 258 or (resid 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 through 265 or (resid 2 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 267 through \ 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) or r \ esid 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 285 or (resid 286 through 287 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 or (resid 289 and (name N or name CA or \ name C or name O or name CB )) or resid 290 through 302 or (resid 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 or (resid 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 326 or \ (resid 327 and (name N or name CA or name C or name O or name CB )) or resid 328 \ or (resid 329 and (name N or name CA or name C or name O or name CB )) or resid \ 330 or (resid 331 through 332 and (name N or name CA or name C or name O or nam \ e CB )) or resid 333 through 345 or (resid 346 and (name N or name CA or name C \ or name O or name CB )) or resid 347 through 356 or (resid 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 364 or resid 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.010 Extract box with map and model: 1.760 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 59.310 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.211 21843 Z= 0.744 Angle : 1.157 19.005 29696 Z= 0.586 Chirality : 0.048 0.270 3518 Planarity : 0.010 0.211 3635 Dihedral : 18.503 178.849 7843 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % 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: -0.87 (0.16), residues: 2796 helix: 0.95 (0.15), residues: 1288 sheet: -0.75 (0.32), residues: 239 loop : -2.24 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E1214 HIS 0.009 0.001 HIS D 269 PHE 0.020 0.002 PHE C 76 TYR 0.016 0.002 TYR E 228 ARG 0.009 0.001 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.8790 (ptp-170) cc_final: 0.8438 (ptp90) REVERT: A 151 GLU cc_start: 0.8538 (tp30) cc_final: 0.8290 (tp30) REVERT: A 205 LYS cc_start: 0.8850 (mmpt) cc_final: 0.8638 (mmtt) REVERT: B 48 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7981 (ptpp) REVERT: B 185 HIS cc_start: 0.7950 (t-90) cc_final: 0.7691 (t-90) REVERT: B 216 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7040 (ttp-170) REVERT: B 222 SER cc_start: 0.8980 (m) cc_final: 0.8240 (p) REVERT: B 232 LYS cc_start: 0.8810 (tttt) cc_final: 0.8576 (tttm) REVERT: B 288 GLN cc_start: 0.7846 (tp40) cc_final: 0.7453 (tp40) REVERT: B 325 VAL cc_start: 0.9154 (p) cc_final: 0.8943 (m) REVERT: C 125 ARG cc_start: 0.8401 (ptp-170) cc_final: 0.8152 (ptp90) REVERT: C 163 ASN cc_start: 0.8608 (m-40) cc_final: 0.8238 (m110) REVERT: C 195 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7390 (ttp-110) REVERT: C 222 SER cc_start: 0.9188 (m) cc_final: 0.8812 (p) REVERT: C 231 LYS cc_start: 0.8270 (mttm) cc_final: 0.7995 (mmmt) REVERT: C 284 ASP cc_start: 0.7068 (m-30) cc_final: 0.6838 (m-30) REVERT: C 319 GLN cc_start: 0.8685 (pt0) cc_final: 0.8226 (pt0) REVERT: D 37 ILE cc_start: 0.9449 (pt) cc_final: 0.9217 (pt) REVERT: D 217 LYS cc_start: 0.8424 (tttt) cc_final: 0.7768 (mtmm) REVERT: D 273 LYS cc_start: 0.8768 (mttt) cc_final: 0.8154 (mtmm) REVERT: D 287 ASN cc_start: 0.8653 (t0) cc_final: 0.8433 (t0) REVERT: D 338 ASP cc_start: 0.8239 (t70) cc_final: 0.7689 (t0) REVERT: E 110 MET cc_start: 0.8049 (mmm) cc_final: 0.7695 (mmt) REVERT: E 156 TRP cc_start: 0.7307 (t-100) cc_final: 0.6852 (t60) REVERT: E 211 LEU cc_start: 0.8272 (tp) cc_final: 0.8042 (tp) REVERT: E 285 ILE cc_start: 0.8779 (mm) cc_final: 0.8431 (mm) REVERT: E 346 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7173 (tm-30) REVERT: E 360 ILE cc_start: 0.9156 (pt) cc_final: 0.8908 (mt) REVERT: E 434 MET cc_start: 0.7478 (mtt) cc_final: 0.7221 (mtp) REVERT: E 479 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7902 (tptm) REVERT: E 497 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7491 (tttm) REVERT: E 527 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8294 (ttpp) REVERT: E 972 LYS cc_start: 0.5979 (tptp) cc_final: 0.4969 (ptpt) REVERT: E 976 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7219 (mmtm) REVERT: E 1108 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7674 (tm-30) REVERT: E 1395 PHE cc_start: 0.8295 (m-80) cc_final: 0.7898 (m-80) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3626 time to fit residues: 333.3446 Evaluate side-chains 533 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 203 ASN B 344 ASN D 183 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21843 Z= 0.217 Angle : 0.549 9.945 29696 Z= 0.279 Chirality : 0.044 0.254 3518 Planarity : 0.004 0.046 3635 Dihedral : 19.005 179.394 3911 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.75 % Allowed : 16.86 % Favored : 80.39 % 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: -0.34 (0.16), residues: 2796 helix: 1.40 (0.15), residues: 1300 sheet: -0.64 (0.32), residues: 237 loop : -1.98 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1214 HIS 0.004 0.001 HIS A 269 PHE 0.017 0.001 PHE A 76 TYR 0.017 0.001 TYR E 121 ARG 0.005 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 554 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.8688 (ptp-170) cc_final: 0.8347 (ptp90) REVERT: A 205 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8574 (mmtt) REVERT: B 48 LYS cc_start: 0.8279 (ptpt) cc_final: 0.8026 (ptpp) REVERT: B 150 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: B 174 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8628 (tp) REVERT: B 205 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7080 (tptp) REVERT: B 232 LYS cc_start: 0.8808 (tttt) cc_final: 0.8572 (tttm) REVERT: B 288 GLN cc_start: 0.7763 (tp40) cc_final: 0.7372 (tp40) REVERT: C 195 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.6980 (ttm110) REVERT: C 222 SER cc_start: 0.9167 (m) cc_final: 0.8748 (p) REVERT: C 231 LYS cc_start: 0.8116 (mttm) cc_final: 0.7848 (mmmt) REVERT: C 319 GLN cc_start: 0.8624 (pt0) cc_final: 0.8167 (pt0) REVERT: D 217 LYS cc_start: 0.8429 (tttt) cc_final: 0.7734 (mtmm) REVERT: D 269 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: D 273 LYS cc_start: 0.8773 (mttt) cc_final: 0.8138 (mtmm) REVERT: D 287 ASN cc_start: 0.8491 (t0) cc_final: 0.8258 (t0) REVERT: D 338 ASP cc_start: 0.8142 (t70) cc_final: 0.7892 (t0) REVERT: E 110 MET cc_start: 0.8027 (mmm) cc_final: 0.7669 (mmt) REVERT: E 156 TRP cc_start: 0.7295 (t-100) cc_final: 0.6803 (t60) REVERT: E 228 TYR cc_start: 0.9211 (m-80) cc_final: 0.8712 (m-80) REVERT: E 344 PHE cc_start: 0.8737 (t80) cc_final: 0.8335 (t80) REVERT: E 346 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7201 (tm-30) REVERT: E 434 MET cc_start: 0.7426 (mtt) cc_final: 0.7087 (mtp) REVERT: E 479 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7904 (tptm) REVERT: E 497 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7469 (tttm) REVERT: E 527 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8243 (ttpp) REVERT: E 972 LYS cc_start: 0.5870 (tptp) cc_final: 0.4943 (ptpt) REVERT: E 976 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7199 (mmtm) REVERT: E 1108 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 1216 GLU cc_start: 0.8075 (tt0) cc_final: 0.7835 (tt0) REVERT: E 1395 PHE cc_start: 0.8319 (m-80) cc_final: 0.7917 (m-80) outliers start: 52 outliers final: 32 residues processed: 581 average time/residue: 0.3558 time to fit residues: 313.1948 Evaluate side-chains 564 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 529 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 chunk 252 optimal weight: 7.9990 chunk 273 optimal weight: 0.0050 chunk 225 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 202 optimal weight: 40.0000 overall best weight: 4.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 203 ASN B 344 ASN C 163 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21843 Z= 0.264 Angle : 0.552 11.045 29696 Z= 0.281 Chirality : 0.044 0.239 3518 Planarity : 0.004 0.045 3635 Dihedral : 18.149 178.902 3911 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.65 % Allowed : 17.76 % Favored : 78.59 % 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: -0.21 (0.16), residues: 2796 helix: 1.47 (0.15), residues: 1299 sheet: -0.39 (0.33), residues: 232 loop : -1.90 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1214 HIS 0.004 0.001 HIS D 269 PHE 0.019 0.001 PHE D 208 TYR 0.016 0.001 TYR E 121 ARG 0.004 0.000 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 540 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.8721 (ptp-170) cc_final: 0.8478 (ptp90) REVERT: A 205 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8568 (mmtt) REVERT: B 48 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8055 (ptpp) REVERT: B 150 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: B 174 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8699 (tp) REVERT: B 232 LYS cc_start: 0.8827 (tttt) cc_final: 0.8626 (tttm) REVERT: B 288 GLN cc_start: 0.7746 (tp40) cc_final: 0.7347 (tp40) REVERT: C 163 ASN cc_start: 0.8570 (m-40) cc_final: 0.8271 (m110) REVERT: C 195 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6937 (ttm110) REVERT: C 222 SER cc_start: 0.9121 (m) cc_final: 0.8746 (p) REVERT: C 231 LYS cc_start: 0.8123 (mttm) cc_final: 0.7868 (mmmt) REVERT: C 319 GLN cc_start: 0.8646 (pt0) cc_final: 0.8155 (pt0) REVERT: D 217 LYS cc_start: 0.8383 (tttt) cc_final: 0.7716 (mtmm) REVERT: D 269 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7285 (t-90) REVERT: D 273 LYS cc_start: 0.8715 (mttt) cc_final: 0.8164 (mtmt) REVERT: D 287 ASN cc_start: 0.8474 (t0) cc_final: 0.8254 (t0) REVERT: D 338 ASP cc_start: 0.8173 (t70) cc_final: 0.7848 (t0) REVERT: E 8 ASN cc_start: 0.8330 (t160) cc_final: 0.8062 (t0) REVERT: E 110 MET cc_start: 0.8060 (mmm) cc_final: 0.7682 (mmt) REVERT: E 156 TRP cc_start: 0.7251 (t-100) cc_final: 0.6749 (t60) REVERT: E 344 PHE cc_start: 0.8747 (t80) cc_final: 0.8355 (t80) REVERT: E 346 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7166 (tm-30) REVERT: E 434 MET cc_start: 0.7420 (mtt) cc_final: 0.7101 (mtp) REVERT: E 479 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7796 (tptm) REVERT: E 497 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7460 (tttm) REVERT: E 527 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8245 (ttpp) REVERT: E 972 LYS cc_start: 0.5901 (tptp) cc_final: 0.4947 (ptpt) REVERT: E 976 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7206 (mmtm) REVERT: E 1065 HIS cc_start: 0.8303 (t-90) cc_final: 0.8095 (t-170) REVERT: E 1108 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 1216 GLU cc_start: 0.8083 (tt0) cc_final: 0.7785 (tt0) REVERT: E 1395 PHE cc_start: 0.8333 (m-80) cc_final: 0.7983 (m-80) outliers start: 69 outliers final: 48 residues processed: 576 average time/residue: 0.3347 time to fit residues: 296.3850 Evaluate side-chains 575 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 524 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 253 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 132 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21843 Z= 0.388 Angle : 0.608 11.583 29696 Z= 0.308 Chirality : 0.046 0.250 3518 Planarity : 0.004 0.049 3635 Dihedral : 17.819 179.752 3911 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.44 % Allowed : 18.82 % Favored : 76.74 % 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: -0.38 (0.16), residues: 2796 helix: 1.28 (0.15), residues: 1299 sheet: -0.47 (0.32), residues: 237 loop : -1.92 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E1214 HIS 0.005 0.001 HIS D 269 PHE 0.023 0.002 PHE D 208 TYR 0.015 0.002 TYR E 228 ARG 0.005 0.001 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 525 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 105 MET cc_start: 0.7411 (ttm) cc_final: 0.7188 (mtt) REVERT: A 205 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8571 (mmtt) REVERT: A 317 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: A 319 GLN cc_start: 0.8214 (mt0) cc_final: 0.7624 (mt0) REVERT: B 48 LYS cc_start: 0.8335 (ptpt) cc_final: 0.8074 (ptpp) REVERT: B 150 GLU cc_start: 0.7983 (pt0) cc_final: 0.7687 (pt0) REVERT: B 209 MET cc_start: 0.8396 (ptp) cc_final: 0.8028 (ptp) REVERT: B 232 LYS cc_start: 0.8845 (tttt) cc_final: 0.8636 (tttm) REVERT: B 288 GLN cc_start: 0.7747 (tp40) cc_final: 0.7365 (tp40) REVERT: B 319 GLN cc_start: 0.8328 (mt0) cc_final: 0.8093 (mt0) REVERT: B 357 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7422 (mp0) REVERT: C 163 ASN cc_start: 0.8625 (m-40) cc_final: 0.8297 (m110) REVERT: C 195 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.6966 (ttm110) REVERT: C 222 SER cc_start: 0.9166 (m) cc_final: 0.8811 (p) REVERT: C 231 LYS cc_start: 0.8149 (mttm) cc_final: 0.7893 (mmmt) REVERT: C 319 GLN cc_start: 0.8689 (pt0) cc_final: 0.8206 (pt0) REVERT: D 269 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7325 (t-90) REVERT: D 273 LYS cc_start: 0.8714 (mttt) cc_final: 0.8169 (mtmt) REVERT: D 287 ASN cc_start: 0.8510 (t0) cc_final: 0.8264 (t0) REVERT: D 338 ASP cc_start: 0.8256 (t70) cc_final: 0.7858 (t0) REVERT: E 8 ASN cc_start: 0.8440 (t160) cc_final: 0.8145 (t0) REVERT: E 110 MET cc_start: 0.8153 (mmm) cc_final: 0.7728 (mmt) REVERT: E 156 TRP cc_start: 0.7263 (t-100) cc_final: 0.6758 (t60) REVERT: E 289 MET cc_start: 0.8900 (mtt) cc_final: 0.8622 (mtt) REVERT: E 344 PHE cc_start: 0.8772 (t80) cc_final: 0.8359 (t80) REVERT: E 346 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7198 (tm-30) REVERT: E 434 MET cc_start: 0.7454 (mtt) cc_final: 0.7252 (mtp) REVERT: E 479 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7867 (tptm) REVERT: E 497 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7457 (tttm) REVERT: E 527 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8206 (ttpp) REVERT: E 972 LYS cc_start: 0.5945 (tptp) cc_final: 0.4953 (ptpt) REVERT: E 976 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7329 (mmtm) REVERT: E 1108 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7646 (tm-30) REVERT: E 1194 MET cc_start: 0.9168 (tmm) cc_final: 0.8794 (tmm) REVERT: E 1395 PHE cc_start: 0.8440 (m-80) cc_final: 0.8032 (m-80) outliers start: 84 outliers final: 70 residues processed: 571 average time/residue: 0.3372 time to fit residues: 295.7940 Evaluate side-chains 590 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 517 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 387 MET Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 200 optimal weight: 40.0000 chunk 110 optimal weight: 0.3980 chunk 229 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21843 Z= 0.164 Angle : 0.499 9.745 29696 Z= 0.254 Chirality : 0.043 0.300 3518 Planarity : 0.004 0.043 3635 Dihedral : 16.767 178.599 3911 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.75 % Allowed : 21.19 % Favored : 76.06 % 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: 0.09 (0.16), residues: 2796 helix: 1.71 (0.15), residues: 1303 sheet: -0.34 (0.32), residues: 235 loop : -1.72 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1214 HIS 0.003 0.001 HIS D 269 PHE 0.017 0.001 PHE A 76 TYR 0.015 0.001 TYR E 121 ARG 0.006 0.000 ARG E 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 535 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9230 (mt) cc_final: 0.8966 (mt) REVERT: A 205 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8596 (mmtp) REVERT: A 317 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: B 48 LYS cc_start: 0.8269 (ptpt) cc_final: 0.8039 (ptpp) REVERT: B 150 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: B 209 MET cc_start: 0.8209 (ptp) cc_final: 0.7974 (ptp) REVERT: B 288 GLN cc_start: 0.7656 (tp40) cc_final: 0.7422 (tp40) REVERT: B 319 GLN cc_start: 0.8252 (mt0) cc_final: 0.7900 (mt0) REVERT: B 356 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8120 (tpp80) REVERT: B 357 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7424 (mp0) REVERT: C 195 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.6912 (ttm110) REVERT: C 222 SER cc_start: 0.9024 (m) cc_final: 0.8661 (p) REVERT: C 231 LYS cc_start: 0.8092 (tttm) cc_final: 0.7871 (mmmt) REVERT: C 319 GLN cc_start: 0.8655 (pt0) cc_final: 0.8195 (pt0) REVERT: D 273 LYS cc_start: 0.8688 (mttt) cc_final: 0.8256 (mtmt) REVERT: D 287 ASN cc_start: 0.8411 (t0) cc_final: 0.8069 (t0) REVERT: D 338 ASP cc_start: 0.8183 (t70) cc_final: 0.7867 (t0) REVERT: E 8 ASN cc_start: 0.8333 (t160) cc_final: 0.8123 (t0) REVERT: E 110 MET cc_start: 0.8019 (mmm) cc_final: 0.7623 (mmt) REVERT: E 156 TRP cc_start: 0.7270 (t-100) cc_final: 0.6723 (t60) REVERT: E 228 TYR cc_start: 0.9171 (m-80) cc_final: 0.8703 (m-80) REVERT: E 344 PHE cc_start: 0.8743 (t80) cc_final: 0.8368 (t80) REVERT: E 346 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7079 (tm-30) REVERT: E 434 MET cc_start: 0.7334 (mtt) cc_final: 0.7133 (mtp) REVERT: E 479 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7688 (tptm) REVERT: E 497 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7414 (tttm) REVERT: E 527 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8254 (ttpp) REVERT: E 603 ASN cc_start: 0.8733 (m-40) cc_final: 0.8443 (m-40) REVERT: E 972 LYS cc_start: 0.5808 (tptp) cc_final: 0.4909 (ptpt) REVERT: E 976 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7269 (mmtm) REVERT: E 1065 HIS cc_start: 0.8278 (t-90) cc_final: 0.8074 (t-170) REVERT: E 1108 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 1395 PHE cc_start: 0.8500 (m-80) cc_final: 0.8094 (m-80) outliers start: 52 outliers final: 31 residues processed: 565 average time/residue: 0.3346 time to fit residues: 292.3516 Evaluate side-chains 551 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 518 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 387 MET Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 268 optimal weight: 0.0870 chunk 223 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 344 ASN C 163 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21843 Z= 0.216 Angle : 0.520 9.653 29696 Z= 0.263 Chirality : 0.043 0.297 3518 Planarity : 0.004 0.041 3635 Dihedral : 16.385 179.736 3911 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.28 % Allowed : 21.83 % Favored : 74.89 % 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: 0.14 (0.16), residues: 2796 helix: 1.72 (0.15), residues: 1305 sheet: -0.31 (0.32), residues: 236 loop : -1.66 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1214 HIS 0.003 0.001 HIS D 269 PHE 0.018 0.001 PHE D 208 TYR 0.015 0.001 TYR E 121 ARG 0.007 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 526 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: A 81 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 205 LYS cc_start: 0.8834 (mmpt) cc_final: 0.8591 (mmtp) REVERT: A 317 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: B 48 LYS cc_start: 0.8290 (ptpt) cc_final: 0.8057 (ptpp) REVERT: B 209 MET cc_start: 0.8309 (ptp) cc_final: 0.8056 (ptp) REVERT: B 288 GLN cc_start: 0.7713 (tp40) cc_final: 0.7488 (tp40) REVERT: B 357 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7429 (mp0) REVERT: C 195 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.6895 (ttm110) REVERT: C 222 SER cc_start: 0.9042 (m) cc_final: 0.8724 (p) REVERT: C 231 LYS cc_start: 0.8098 (tttm) cc_final: 0.7863 (mmmt) REVERT: C 319 GLN cc_start: 0.8703 (pt0) cc_final: 0.8229 (pt0) REVERT: D 269 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: D 273 LYS cc_start: 0.8764 (mttt) cc_final: 0.8271 (mtmt) REVERT: D 287 ASN cc_start: 0.8432 (t0) cc_final: 0.8190 (t0) REVERT: D 338 ASP cc_start: 0.8248 (t70) cc_final: 0.7856 (t0) REVERT: E 8 ASN cc_start: 0.8307 (t160) cc_final: 0.8105 (t0) REVERT: E 110 MET cc_start: 0.8095 (mmm) cc_final: 0.7644 (mmt) REVERT: E 156 TRP cc_start: 0.7184 (t-100) cc_final: 0.6756 (t60) REVERT: E 228 TYR cc_start: 0.9199 (m-80) cc_final: 0.8707 (m-80) REVERT: E 271 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: E 344 PHE cc_start: 0.8751 (t80) cc_final: 0.8379 (t80) REVERT: E 346 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7044 (tm-30) REVERT: E 479 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7689 (tptm) REVERT: E 497 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7475 (tttm) REVERT: E 603 ASN cc_start: 0.8787 (m-40) cc_final: 0.8521 (m-40) REVERT: E 972 LYS cc_start: 0.5878 (tptp) cc_final: 0.4901 (ptpt) REVERT: E 976 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7293 (mmtm) REVERT: E 1065 HIS cc_start: 0.8245 (t-90) cc_final: 0.8043 (t-170) REVERT: E 1108 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7641 (tm-30) REVERT: E 1194 MET cc_start: 0.9086 (tmm) cc_final: 0.8749 (tmm) REVERT: E 1395 PHE cc_start: 0.8547 (m-80) cc_final: 0.8146 (m-80) outliers start: 62 outliers final: 47 residues processed: 557 average time/residue: 0.3313 time to fit residues: 284.9498 Evaluate side-chains 570 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 518 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 387 MET Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1275 VAL Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 226 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 245 GLN B 196 HIS B 344 ASN C 163 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21843 Z= 0.391 Angle : 0.601 9.550 29696 Z= 0.305 Chirality : 0.046 0.288 3518 Planarity : 0.004 0.047 3635 Dihedral : 16.498 176.586 3911 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.55 % Allowed : 21.67 % Favored : 73.78 % 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: -0.19 (0.16), residues: 2796 helix: 1.40 (0.15), residues: 1303 sheet: -0.46 (0.32), residues: 235 loop : -1.77 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1214 HIS 0.012 0.001 HIS B 196 PHE 0.026 0.002 PHE D 208 TYR 0.014 0.002 TYR E1250 ARG 0.006 0.001 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 526 time to evaluate : 2.248 Fit side-chains revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 67 LEU cc_start: 0.9241 (mt) cc_final: 0.9014 (mt) REVERT: A 81 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 205 LYS cc_start: 0.8801 (mmpt) cc_final: 0.8547 (mmtt) REVERT: A 317 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: A 319 GLN cc_start: 0.8238 (mt0) cc_final: 0.7772 (mt0) REVERT: B 48 LYS cc_start: 0.8382 (ptpt) cc_final: 0.8135 (ptpp) REVERT: B 151 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6713 (tm-30) REVERT: B 209 MET cc_start: 0.8441 (ptp) cc_final: 0.8055 (ptp) REVERT: B 288 GLN cc_start: 0.7742 (tp40) cc_final: 0.7347 (tp40) REVERT: B 357 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7423 (mp0) REVERT: C 163 ASN cc_start: 0.8680 (m-40) cc_final: 0.8388 (m110) REVERT: C 195 ARG cc_start: 0.7440 (ttp-110) cc_final: 0.6969 (ttm110) REVERT: C 222 SER cc_start: 0.9079 (m) cc_final: 0.8765 (p) REVERT: C 231 LYS cc_start: 0.8115 (tttm) cc_final: 0.7856 (mmmt) REVERT: C 319 GLN cc_start: 0.8717 (pt0) cc_final: 0.8241 (pt0) REVERT: D 269 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7213 (t-90) REVERT: D 273 LYS cc_start: 0.8787 (mttt) cc_final: 0.8289 (mtmt) REVERT: D 287 ASN cc_start: 0.8502 (t0) cc_final: 0.8260 (t0) REVERT: D 338 ASP cc_start: 0.8256 (t70) cc_final: 0.7862 (t0) REVERT: E 8 ASN cc_start: 0.8402 (t160) cc_final: 0.8192 (t0) REVERT: E 110 MET cc_start: 0.8147 (mmm) cc_final: 0.7708 (mmt) REVERT: E 156 TRP cc_start: 0.7321 (t-100) cc_final: 0.6798 (t60) REVERT: E 271 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: E 344 PHE cc_start: 0.8767 (t80) cc_final: 0.8375 (t80) REVERT: E 346 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7173 (tm-30) REVERT: E 479 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7711 (tptm) REVERT: E 497 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7498 (tttm) REVERT: E 603 ASN cc_start: 0.8729 (m-40) cc_final: 0.8387 (m-40) REVERT: E 972 LYS cc_start: 0.5958 (tptp) cc_final: 0.4932 (ptpt) REVERT: E 976 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7359 (mmtm) REVERT: E 1056 MET cc_start: 0.8334 (tmm) cc_final: 0.7648 (tmm) REVERT: E 1065 HIS cc_start: 0.8355 (t-90) cc_final: 0.8140 (t-170) REVERT: E 1108 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 1194 MET cc_start: 0.9163 (tmm) cc_final: 0.8774 (tmm) REVERT: E 1395 PHE cc_start: 0.8488 (m-80) cc_final: 0.8081 (m-80) outliers start: 86 outliers final: 68 residues processed: 574 average time/residue: 0.3350 time to fit residues: 297.5379 Evaluate side-chains 593 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 520 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 387 MET Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1275 VAL Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 170 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 210 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 319 GLN B 344 ASN D 245 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21843 Z= 0.131 Angle : 0.497 10.432 29696 Z= 0.252 Chirality : 0.042 0.283 3518 Planarity : 0.004 0.043 3635 Dihedral : 15.543 175.110 3911 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.64 % Allowed : 23.52 % Favored : 73.84 % 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: 0.34 (0.16), residues: 2796 helix: 1.89 (0.15), residues: 1300 sheet: -0.31 (0.33), residues: 236 loop : -1.54 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 229 HIS 0.013 0.001 HIS A 244 PHE 0.017 0.001 PHE E1131 TYR 0.023 0.001 TYR E 121 ARG 0.008 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 540 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 67 LEU cc_start: 0.9162 (mt) cc_final: 0.8935 (mt) REVERT: A 168 ILE cc_start: 0.9482 (mm) cc_final: 0.9039 (mt) REVERT: A 205 LYS cc_start: 0.8778 (mmpt) cc_final: 0.8542 (mmtp) REVERT: A 317 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: B 45 LEU cc_start: 0.9207 (mt) cc_final: 0.8950 (mp) REVERT: B 48 LYS cc_start: 0.8255 (ptpt) cc_final: 0.8044 (ptpp) REVERT: B 209 MET cc_start: 0.8327 (ptp) cc_final: 0.7965 (ptp) REVERT: B 288 GLN cc_start: 0.7633 (tp40) cc_final: 0.7424 (tp40) REVERT: B 356 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7720 (tpp80) REVERT: B 357 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7449 (mp0) REVERT: C 195 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.6887 (ttm110) REVERT: C 205 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7498 (ttmt) REVERT: C 222 SER cc_start: 0.8972 (m) cc_final: 0.8649 (p) REVERT: C 231 LYS cc_start: 0.8062 (tttm) cc_final: 0.7841 (mmmt) REVERT: C 296 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 319 GLN cc_start: 0.8696 (pt0) cc_final: 0.8210 (pt0) REVERT: D 273 LYS cc_start: 0.8758 (mttt) cc_final: 0.8263 (mtmt) REVERT: D 287 ASN cc_start: 0.8369 (t0) cc_final: 0.8024 (t0) REVERT: E 110 MET cc_start: 0.7937 (mmm) cc_final: 0.7548 (mmt) REVERT: E 156 TRP cc_start: 0.7328 (t-100) cc_final: 0.6861 (t60) REVERT: E 228 TYR cc_start: 0.9103 (m-80) cc_final: 0.8695 (m-80) REVERT: E 271 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: E 344 PHE cc_start: 0.8736 (t80) cc_final: 0.8363 (t80) REVERT: E 346 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7038 (tm-30) REVERT: E 479 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7673 (tptm) REVERT: E 497 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7457 (tttm) REVERT: E 603 ASN cc_start: 0.8676 (m-40) cc_final: 0.8382 (m-40) REVERT: E 881 MET cc_start: 0.4111 (mmm) cc_final: 0.3509 (tpp) REVERT: E 972 LYS cc_start: 0.5782 (tptp) cc_final: 0.4868 (ptpt) REVERT: E 976 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7467 (tptt) REVERT: E 1056 MET cc_start: 0.8180 (tmm) cc_final: 0.7560 (tmm) REVERT: E 1065 HIS cc_start: 0.8134 (t-90) cc_final: 0.7923 (t-170) REVERT: E 1108 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7631 (tm-30) REVERT: E 1216 GLU cc_start: 0.8086 (tt0) cc_final: 0.7806 (tt0) REVERT: E 1395 PHE cc_start: 0.8498 (m-80) cc_final: 0.8094 (m-80) outliers start: 50 outliers final: 36 residues processed: 568 average time/residue: 0.3459 time to fit residues: 301.8318 Evaluate side-chains 566 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 526 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1275 VAL Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 9.9990 chunk 256 optimal weight: 40.0000 chunk 234 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN C 163 ASN D 245 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21843 Z= 0.168 Angle : 0.510 10.394 29696 Z= 0.257 Chirality : 0.042 0.288 3518 Planarity : 0.004 0.043 3635 Dihedral : 15.169 172.501 3911 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 23.73 % Favored : 73.78 % 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: 0.39 (0.16), residues: 2796 helix: 1.93 (0.15), residues: 1303 sheet: -0.39 (0.32), residues: 244 loop : -1.49 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1214 HIS 0.005 0.001 HIS D 244 PHE 0.019 0.001 PHE D 208 TYR 0.018 0.001 TYR E 121 ARG 0.008 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 534 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: A 67 LEU cc_start: 0.9170 (mt) cc_final: 0.8939 (mt) REVERT: A 168 ILE cc_start: 0.9472 (mm) cc_final: 0.9032 (mt) REVERT: A 205 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8548 (mmtp) REVERT: A 317 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: B 48 LYS cc_start: 0.8269 (ptpt) cc_final: 0.8052 (ptpp) REVERT: B 209 MET cc_start: 0.8264 (ptp) cc_final: 0.7968 (ptp) REVERT: B 288 GLN cc_start: 0.7635 (tp40) cc_final: 0.7393 (tp40) REVERT: B 356 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7693 (tpp80) REVERT: B 357 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7421 (mp0) REVERT: C 195 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6905 (ttm110) REVERT: C 205 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7685 (mttt) REVERT: C 222 SER cc_start: 0.8980 (m) cc_final: 0.8693 (p) REVERT: C 231 LYS cc_start: 0.8068 (tttm) cc_final: 0.7833 (mmmt) REVERT: C 296 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 319 GLN cc_start: 0.8734 (pt0) cc_final: 0.8240 (pt0) REVERT: D 273 LYS cc_start: 0.8789 (mttt) cc_final: 0.8285 (mtmt) REVERT: D 287 ASN cc_start: 0.8409 (t0) cc_final: 0.8091 (t0) REVERT: E 110 MET cc_start: 0.8021 (mmm) cc_final: 0.7608 (mmt) REVERT: E 156 TRP cc_start: 0.7302 (t-100) cc_final: 0.6982 (t60) REVERT: E 228 TYR cc_start: 0.9171 (m-80) cc_final: 0.8698 (m-80) REVERT: E 271 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: E 344 PHE cc_start: 0.8764 (t80) cc_final: 0.8381 (t80) REVERT: E 346 GLU cc_start: 0.7585 (tm-30) cc_final: 0.6999 (tm-30) REVERT: E 479 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7661 (tptm) REVERT: E 497 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7426 (tttm) REVERT: E 603 ASN cc_start: 0.8628 (m-40) cc_final: 0.8343 (m-40) REVERT: E 881 MET cc_start: 0.4240 (mmm) cc_final: 0.3660 (tpp) REVERT: E 972 LYS cc_start: 0.5961 (tptp) cc_final: 0.4945 (ptpt) REVERT: E 976 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7488 (tptt) REVERT: E 1056 MET cc_start: 0.8249 (tmm) cc_final: 0.7641 (tmm) REVERT: E 1065 HIS cc_start: 0.8248 (t-90) cc_final: 0.8026 (t-170) REVERT: E 1108 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 1395 PHE cc_start: 0.8501 (m-80) cc_final: 0.8144 (m-80) outliers start: 47 outliers final: 39 residues processed: 560 average time/residue: 0.3384 time to fit residues: 295.4658 Evaluate side-chains 562 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 519 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 120 CYS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1275 VAL Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.9990 chunk 264 optimal weight: 0.0070 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 20.0000 chunk 276 optimal weight: 0.0270 chunk 254 optimal weight: 8.9990 chunk 220 optimal weight: 50.0000 chunk 22 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN D 246 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN E 103 HIS E 124 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 21843 Z= 0.134 Angle : 0.502 11.850 29696 Z= 0.250 Chirality : 0.042 0.290 3518 Planarity : 0.004 0.043 3635 Dihedral : 14.470 169.790 3911 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.80 % Allowed : 24.52 % Favored : 73.68 % 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: 0.57 (0.16), residues: 2796 helix: 2.09 (0.15), residues: 1297 sheet: -0.27 (0.32), residues: 244 loop : -1.40 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 229 HIS 0.013 0.001 HIS D 244 PHE 0.018 0.001 PHE E1131 TYR 0.021 0.001 TYR E 121 ARG 0.010 0.000 ARG E 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 528 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9155 (mt) cc_final: 0.8936 (mt) REVERT: A 168 ILE cc_start: 0.9391 (mm) cc_final: 0.8980 (mt) REVERT: A 205 LYS cc_start: 0.8802 (mmpt) cc_final: 0.8569 (mmtp) REVERT: A 317 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: B 56 PHE cc_start: 0.7033 (m-80) cc_final: 0.6717 (m-80) REVERT: B 90 MET cc_start: 0.7575 (mtt) cc_final: 0.7372 (mtt) REVERT: B 209 MET cc_start: 0.8216 (ptp) cc_final: 0.7745 (ptp) REVERT: B 288 GLN cc_start: 0.7573 (tp40) cc_final: 0.7333 (tp40) REVERT: B 356 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7678 (tpp80) REVERT: B 357 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7436 (mp0) REVERT: C 74 VAL cc_start: 0.8647 (t) cc_final: 0.8394 (p) REVERT: C 195 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.6849 (ttm110) REVERT: C 205 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7634 (tttt) REVERT: C 222 SER cc_start: 0.8957 (m) cc_final: 0.8669 (p) REVERT: C 296 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8763 (tt) REVERT: C 319 GLN cc_start: 0.8655 (pt0) cc_final: 0.8150 (pt0) REVERT: D 273 LYS cc_start: 0.8757 (mttt) cc_final: 0.8265 (mtmt) REVERT: D 287 ASN cc_start: 0.8318 (t0) cc_final: 0.7990 (t0) REVERT: E 96 GLN cc_start: 0.7108 (mt0) cc_final: 0.6318 (tm-30) REVERT: E 110 MET cc_start: 0.7889 (mmm) cc_final: 0.7510 (mmt) REVERT: E 156 TRP cc_start: 0.7291 (t-100) cc_final: 0.6843 (t60) REVERT: E 228 TYR cc_start: 0.9087 (m-80) cc_final: 0.8679 (m-80) REVERT: E 271 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: E 344 PHE cc_start: 0.8692 (t80) cc_final: 0.8329 (t80) REVERT: E 346 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7067 (tm-30) REVERT: E 479 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7630 (tptm) REVERT: E 497 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7330 (tttm) REVERT: E 603 ASN cc_start: 0.8543 (m-40) cc_final: 0.8259 (m-40) REVERT: E 881 MET cc_start: 0.4003 (mmm) cc_final: 0.3427 (tpp) REVERT: E 972 LYS cc_start: 0.5927 (tptp) cc_final: 0.5044 (ptpt) REVERT: E 976 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7392 (tptt) REVERT: E 1056 MET cc_start: 0.8207 (tmm) cc_final: 0.7620 (tmm) REVERT: E 1065 HIS cc_start: 0.8249 (t-90) cc_final: 0.8042 (t-170) REVERT: E 1108 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7628 (tm-30) REVERT: E 1395 PHE cc_start: 0.8521 (m-80) cc_final: 0.8134 (m-80) outliers start: 34 outliers final: 26 residues processed: 546 average time/residue: 0.3303 time to fit residues: 280.3753 Evaluate side-chains 547 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 518 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1275 VAL Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 61 optimal weight: 0.4980 chunk 220 optimal weight: 50.0000 chunk 92 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN D 246 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.162899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.129364 restraints weight = 26817.042| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.97 r_work: 0.3115 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21843 Z= 0.346 Angle : 0.573 10.806 29696 Z= 0.289 Chirality : 0.045 0.298 3518 Planarity : 0.004 0.044 3635 Dihedral : 14.797 167.310 3911 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.64 % Allowed : 24.05 % Favored : 73.31 % 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: 0.32 (0.16), residues: 2796 helix: 1.80 (0.15), residues: 1302 sheet: -0.21 (0.33), residues: 239 loop : -1.49 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 980 HIS 0.010 0.001 HIS B 196 PHE 0.023 0.002 PHE D 208 TYR 0.015 0.001 TYR C 335 ARG 0.008 0.001 ARG E 804 =============================================================================== Job complete usr+sys time: 5738.55 seconds wall clock time: 103 minutes 39.75 seconds (6219.75 seconds total)