Starting phenix.real_space_refine on Fri Feb 23 03:07:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yut_34110/02_2024/7yut_34110.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 23028 2.51 5 N 6402 2.21 5 O 6894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 503": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 567": "NH1" <-> "NH2" Residue "E TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 694": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 250": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 366": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 479": "NH1" <-> "NH2" Residue "F ARG 503": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 519": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 567": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F ARG 694": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Time building chain proxies: 17.41, per 1000 atoms: 0.48 Number of scatterers: 36450 At special positions: 0 Unit cell: (159.9, 194.34, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6894 8.00 N 6402 7.00 C 23028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.01 Conformation dependent library (CDL) restraints added in 6.5 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 42 sheets defined 46.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.615A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.795A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 3.579A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.034A pdb=" N ILE A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 236 removed outlier: 3.979A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.731A pdb=" N ASP A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.746A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.537A pdb=" N LYS A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.517A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.895A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.688A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.751A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.107A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.654A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.840A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.511A pdb=" N GLU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.920A pdb=" N GLU A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.732A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.631A pdb=" N GLY C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.585A pdb=" N LEU C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 136 removed outlier: 3.645A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.810A pdb=" N VAL C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 153 " --> pdb=" O GLU C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.774A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 235 removed outlier: 3.752A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.835A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.679A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 4.088A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 424 through 427 removed outlier: 3.555A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 424 through 427' Processing helix chain 'C' and resid 434 through 444 removed outlier: 3.968A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.780A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 515 removed outlier: 3.901A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.617A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 591 removed outlier: 3.516A pdb=" N THR C 590 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 591 " --> pdb=" O ALA C 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 587 through 591' Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.966A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 4.109A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.944A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.889A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 769 removed outlier: 3.661A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 removed outlier: 3.890A pdb=" N LYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 137 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.574A pdb=" N LEU E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 235 removed outlier: 3.579A pdb=" N ARG E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 256 removed outlier: 4.264A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.571A pdb=" N VAL E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.925A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 386 through 391 Processing helix chain 'E' and resid 403 through 412 removed outlier: 4.125A pdb=" N HIS E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 434 through 444 removed outlier: 3.732A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 483 Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 515 Processing helix chain 'E' and resid 523 through 535 removed outlier: 4.090A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.760A pdb=" N GLU E 544 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 579 removed outlier: 4.003A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 646 removed outlier: 3.810A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 removed outlier: 3.525A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 removed outlier: 4.144A pdb=" N TYR E 658 " --> pdb=" O GLU E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 691 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.740A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 740 Processing helix chain 'E' and resid 761 through 768 removed outlier: 3.656A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.598A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.519A pdb=" N GLN D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.696A pdb=" N ALA D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.841A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 234 removed outlier: 3.712A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 207 " --> pdb=" O PHE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.632A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.875A pdb=" N ASP D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.946A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.977A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 391 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.511A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 removed outlier: 4.299A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.502A pdb=" N ASN D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 450' Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.901A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 477 " --> pdb=" O LEU D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 506 through 515 Processing helix chain 'D' and resid 523 through 534 removed outlier: 3.824A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.697A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 591 removed outlier: 4.118A pdb=" N GLU D 591 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.536A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.648A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 761 through 768 removed outlier: 3.786A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 removed outlier: 3.993A pdb=" N ARG F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 138 removed outlier: 3.798A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 172 through 182 Processing helix chain 'F' and resid 185 through 235 removed outlier: 3.777A pdb=" N LYS F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.895A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 280 through 294 removed outlier: 4.015A pdb=" N VAL F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 316 Processing helix chain 'F' and resid 324 through 337 removed outlier: 4.053A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.545A pdb=" N LEU F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 412 Processing helix chain 'F' and resid 423 through 427 removed outlier: 3.800A pdb=" N MET F 427 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 4.101A pdb=" N ALA F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 477 removed outlier: 3.977A pdb=" N THR F 476 " --> pdb=" O THR F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 515 Processing helix chain 'F' and resid 523 through 534 removed outlier: 3.702A pdb=" N ILE F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 560 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 579 removed outlier: 4.132A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 removed outlier: 3.659A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 718 through 728 Processing helix chain 'F' and resid 736 through 745 removed outlier: 4.229A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.965A pdb=" N LEU F 751 " --> pdb=" O PRO F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 768 removed outlier: 3.666A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.934A pdb=" N ARG B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 139 removed outlier: 3.875A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.703A pdb=" N GLU B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 184 through 236 removed outlier: 4.000A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.569A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.801A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.161A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.106A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 removed outlier: 4.025A pdb=" N ASN B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 515 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.918A pdb=" N GLU B 589 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.681A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 3.647A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 4.227A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.986A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.730A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN A 93 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU A 43 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 45 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 44 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 69 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 380 removed outlier: 6.360A pdb=" N LYS A 375 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 420 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 468 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 354 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.586A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 618 Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 removed outlier: 7.057A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.752A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU C 82 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ARG C 76 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL C 84 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL C 86 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS C 72 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TRP C 65 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA C 48 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 5 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 105 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.752A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 91 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 377 through 380 removed outlier: 6.972A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASP C 422 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522 removed outlier: 7.008A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 597 through 600 removed outlier: 3.892A pdb=" N ALA C 597 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 614 through 616 removed outlier: 6.167A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 732 through 736 removed outlier: 7.173A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 7 removed outlier: 4.147A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.575A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 67 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.575A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG E 91 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE E 110 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN E 93 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 378 through 380 removed outlier: 5.773A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.061A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 596 through 597 removed outlier: 3.514A pdb=" N ALA E 597 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 732 through 733 removed outlier: 3.715A pdb=" N ILE E 733 " --> pdb=" O GLU E 755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.886A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 25 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.886A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 354 removed outlier: 3.746A pdb=" N ILE D 488 " --> pdb=" O VAL D 352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 378 through 380 removed outlier: 3.522A pdb=" N ILE D 379 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.486A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 596 through 601 removed outlier: 4.301A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.682A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.843A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.642A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 104 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 106 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP F 96 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.939A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 82 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG F 76 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 84 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA F 74 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL F 86 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS F 72 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TRP F 65 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA F 48 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 375 through 380 removed outlier: 7.623A pdb=" N ILE F 468 " --> pdb=" O PRO F 417 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AD7, first strand: chain 'F' and resid 596 through 601 removed outlier: 3.960A pdb=" N ALA F 615 " --> pdb=" O HIS F 664 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS F 664 " --> pdb=" O ALA F 615 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 662 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL F 665 " --> pdb=" O SER F 624 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 700 through 702 removed outlier: 6.863A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.740A pdb=" N VAL B 47 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA B 48 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP B 65 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.740A pdb=" N VAL B 47 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA B 48 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP B 65 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 66 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 92 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 379 through 380 removed outlier: 6.952A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 599 through 600 Processing sheet with id=AE4, first strand: chain 'B' and resid 613 through 616 removed outlier: 3.541A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 615 " --> pdb=" O HIS B 664 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 705 through 706 removed outlier: 3.855A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 732 through 735 removed outlier: 6.427A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1496 hydrogen bonds defined for protein. 4365 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: 13.00 Time building geometry restraints manager: 14.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11078 1.33 - 1.45: 6155 1.45 - 1.58: 19618 1.58 - 1.70: 1 1.70 - 1.82: 252 Bond restraints: 37104 Sorted by residual: bond pdb=" C ALA A 671 " pdb=" N THR A 672 " ideal model delta sigma weight residual 1.330 1.214 0.116 1.37e-02 5.33e+03 7.20e+01 bond pdb=" C ARG A 479 " pdb=" N PRO A 480 " ideal model delta sigma weight residual 1.337 1.390 -0.053 1.11e-02 8.12e+03 2.28e+01 bond pdb=" C VAL B 712 " pdb=" N MET B 713 " ideal model delta sigma weight residual 1.333 1.218 0.114 2.74e-02 1.33e+03 1.74e+01 bond pdb=" C ASP C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C GLN E 504 " pdb=" N TYR E 505 " ideal model delta sigma weight residual 1.333 1.291 0.042 1.34e-02 5.57e+03 9.89e+00 ... (remaining 37099 not shown) Histogram of bond angle deviations from ideal: 95.13 - 103.38: 571 103.38 - 111.62: 16402 111.62 - 119.86: 16855 119.86 - 128.10: 16140 128.10 - 136.35: 312 Bond angle restraints: 50280 Sorted by residual: angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 112.72 99.60 13.12 1.28e+00 6.10e-01 1.05e+02 angle pdb=" C ALA A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta sigma weight residual 120.60 134.43 -13.83 1.53e+00 4.27e-01 8.17e+01 angle pdb=" C HIS A 319 " pdb=" N TYR A 320 " pdb=" CA TYR A 320 " ideal model delta sigma weight residual 121.31 133.46 -12.15 1.49e+00 4.50e-01 6.65e+01 angle pdb=" C ASP A 457 " pdb=" N VAL A 458 " pdb=" CA VAL A 458 " ideal model delta sigma weight residual 123.33 117.38 5.95 8.70e-01 1.32e+00 4.68e+01 angle pdb=" N ALA B 679 " pdb=" CA ALA B 679 " pdb=" C ALA B 679 " ideal model delta sigma weight residual 111.71 103.42 8.29 1.34e+00 5.57e-01 3.83e+01 ... (remaining 50275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 21460 16.57 - 33.14: 1203 33.14 - 49.71: 204 49.71 - 66.29: 11 66.29 - 82.86: 48 Dihedral angle restraints: 22926 sinusoidal: 9540 harmonic: 13386 Sorted by residual: dihedral pdb=" CA ASP F 51 " pdb=" C ASP F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta harmonic sigma weight residual -180.00 -105.92 -74.08 0 5.00e+00 4.00e-02 2.19e+02 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.96 -71.04 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -113.58 -66.42 0 5.00e+00 4.00e-02 1.76e+02 ... (remaining 22923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5103 0.104 - 0.208: 588 0.208 - 0.312: 30 0.312 - 0.416: 2 0.416 - 0.521: 1 Chirality restraints: 5724 Sorted by residual: chirality pdb=" CB ILE D 574 " pdb=" CA ILE D 574 " pdb=" CG1 ILE D 574 " pdb=" CG2 ILE D 574 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CG LEU C 290 " pdb=" CB LEU C 290 " pdb=" CD1 LEU C 290 " pdb=" CD2 LEU C 290 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CG LEU E 351 " pdb=" CB LEU E 351 " pdb=" CD1 LEU E 351 " pdb=" CD2 LEU E 351 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 5721 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 51 " 0.058 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO E 52 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 52 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 51 " 0.058 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO F 52 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO F 52 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 668 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO F 668 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO F 668 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 669 " -0.020 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1403 2.68 - 3.24: 34795 3.24 - 3.79: 60839 3.79 - 4.35: 77441 4.35 - 4.90: 122419 Nonbonded interactions: 296897 Sorted by model distance: nonbonded pdb=" O PRO E 297 " pdb=" OH TYR E 460 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR C 535 " pdb=" OE1 GLU C 546 " model vdw 2.186 2.440 nonbonded pdb=" O GLU D 260 " pdb=" OG1 THR D 264 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR F 672 " pdb=" O LYS F 674 " model vdw 2.213 2.440 nonbonded pdb=" O PRO B 297 " pdb=" OH TYR B 460 " model vdw 2.239 2.440 ... (remaining 296892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.030 Extract box with map and model: 9.950 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 87.130 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 0.116 37104 Z= 0.639 Angle : 1.337 21.167 50280 Z= 0.758 Chirality : 0.065 0.521 5724 Planarity : 0.009 0.090 6552 Dihedral : 11.311 82.858 14310 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.86 % Favored : 90.94 % Rotamer: Outliers : 0.59 % Allowed : 3.65 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 5.30 % Twisted General : 0.32 % 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: -4.13 (0.10), residues: 4626 helix: -2.56 (0.09), residues: 1915 sheet: -2.34 (0.21), residues: 492 loop : -2.98 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.006 TRP B 563 HIS 0.021 0.005 HIS D 726 PHE 0.033 0.004 PHE A 557 TYR 0.050 0.004 TYR C 651 ARG 0.024 0.002 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 492 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.5686 (mmt) cc_final: 0.5267 (mpp) REVERT: A 446 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9066 (mp0) REVERT: A 633 MET cc_start: 0.8772 (mmm) cc_final: 0.8435 (mtm) REVERT: A 657 PHE cc_start: 0.6603 (p90) cc_final: 0.6300 (p90) REVERT: A 683 MET cc_start: 0.9115 (mtt) cc_final: 0.8794 (mtt) REVERT: C 437 SER cc_start: 0.8720 (m) cc_final: 0.8493 (p) REVERT: C 509 LYS cc_start: 0.8721 (mttm) cc_final: 0.8461 (mptt) REVERT: C 545 ARG cc_start: 0.8770 (mtm180) cc_final: 0.8291 (mmp80) REVERT: C 663 LEU cc_start: 0.8871 (mt) cc_final: 0.8622 (mp) REVERT: C 698 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6150 (pp-130) REVERT: E 430 ASP cc_start: 0.6698 (m-30) cc_final: 0.6263 (p0) REVERT: E 632 VAL cc_start: 0.8710 (m) cc_final: 0.7794 (m) REVERT: E 633 MET cc_start: 0.8457 (mmt) cc_final: 0.8114 (mmt) REVERT: D 38 MET cc_start: 0.1800 (mmt) cc_final: 0.0958 (mtt) REVERT: D 220 ASN cc_start: 0.7154 (m110) cc_final: 0.6849 (m-40) REVERT: D 230 MET cc_start: 0.7077 (ttp) cc_final: 0.6771 (ttp) REVERT: D 536 ARG cc_start: 0.7254 (mmt180) cc_final: 0.6755 (mmt180) REVERT: D 590 THR cc_start: 0.7761 (m) cc_final: 0.7229 (m) REVERT: D 702 MET cc_start: 0.8821 (pmt) cc_final: 0.8377 (pmm) REVERT: F 97 TYR cc_start: 0.7436 (p90) cc_final: 0.7120 (p90) REVERT: F 138 ASN cc_start: 0.7333 (m110) cc_final: 0.7130 (m110) REVERT: F 328 ARG cc_start: 0.8972 (mpt90) cc_final: 0.8521 (mmm-85) REVERT: F 368 ILE cc_start: 0.8800 (mt) cc_final: 0.8540 (mt) REVERT: F 505 TYR cc_start: 0.7654 (m-80) cc_final: 0.7335 (m-10) REVERT: F 625 LEU cc_start: 0.8628 (pt) cc_final: 0.8133 (mp) REVERT: F 633 MET cc_start: 0.9178 (mmt) cc_final: 0.8854 (mtt) REVERT: F 642 THR cc_start: 0.8776 (m) cc_final: 0.8565 (m) REVERT: F 702 MET cc_start: 0.7051 (ptp) cc_final: 0.6521 (pmm) REVERT: B 520 ILE cc_start: 0.7335 (mt) cc_final: 0.7117 (mm) outliers start: 23 outliers final: 7 residues processed: 511 average time/residue: 0.5503 time to fit residues: 432.4078 Evaluate side-chains 317 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 309 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 40.0000 chunk 350 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 419 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 278 GLN A 310 HIS ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A 739 ASN C 73 GLN C 83 GLN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS E 310 HIS ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 346 ASN D 377 HIS D 447 GLN D 472 ASN D 504 GLN ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 739 ASN B 93 GLN B 138 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 377 HIS B 393 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 727 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37104 Z= 0.204 Angle : 0.702 12.940 50280 Z= 0.364 Chirality : 0.044 0.201 5724 Planarity : 0.006 0.077 6552 Dihedral : 6.895 61.838 5106 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.09 % 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: -2.80 (0.11), residues: 4626 helix: -0.98 (0.11), residues: 1977 sheet: -2.07 (0.20), residues: 546 loop : -2.66 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 563 HIS 0.009 0.001 HIS E 666 PHE 0.014 0.001 PHE B 45 TYR 0.025 0.002 TYR B 225 ARG 0.008 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 405 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ILE cc_start: 0.8107 (mp) cc_final: 0.7899 (mp) REVERT: A 633 MET cc_start: 0.8744 (mmm) cc_final: 0.8522 (mtm) REVERT: A 657 PHE cc_start: 0.6814 (p90) cc_final: 0.6480 (p90) REVERT: C 485 MET cc_start: 0.7713 (mpp) cc_final: 0.7143 (pmm) REVERT: C 545 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8323 (mmp80) REVERT: E 430 ASP cc_start: 0.6701 (m-30) cc_final: 0.6185 (m-30) REVERT: E 614 VAL cc_start: 0.7589 (t) cc_final: 0.7371 (t) REVERT: E 633 MET cc_start: 0.8401 (mmt) cc_final: 0.7986 (mmt) REVERT: E 635 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: D 38 MET cc_start: 0.1541 (mmt) cc_final: 0.0764 (mtt) REVERT: D 139 HIS cc_start: 0.6212 (m90) cc_final: 0.4473 (m90) REVERT: D 203 PHE cc_start: 0.7447 (t80) cc_final: 0.7047 (m-80) REVERT: D 258 MET cc_start: 0.2504 (mtt) cc_final: 0.1546 (mtt) REVERT: F 2 ARG cc_start: 0.3705 (mmt90) cc_final: 0.3157 (mtp-110) REVERT: F 97 TYR cc_start: 0.7402 (p90) cc_final: 0.7113 (p90) REVERT: F 146 ARG cc_start: 0.6235 (ptp-170) cc_final: 0.5812 (tpt170) REVERT: F 328 ARG cc_start: 0.8862 (mpt90) cc_final: 0.8601 (mmm160) REVERT: F 516 MET cc_start: 0.3908 (ptm) cc_final: 0.3678 (ptm) REVERT: F 625 LEU cc_start: 0.8551 (pt) cc_final: 0.8022 (mp) REVERT: F 633 MET cc_start: 0.9101 (mmt) cc_final: 0.8826 (mmm) REVERT: F 702 MET cc_start: 0.6937 (ptp) cc_final: 0.6386 (pmm) REVERT: B 318 ASP cc_start: 0.7142 (p0) cc_final: 0.6858 (p0) REVERT: B 333 LEU cc_start: 0.8732 (tp) cc_final: 0.8500 (tt) REVERT: B 379 ILE cc_start: 0.9343 (tp) cc_final: 0.9071 (tt) REVERT: B 421 LEU cc_start: 0.9394 (mt) cc_final: 0.9193 (mt) REVERT: B 427 MET cc_start: 0.7261 (ptp) cc_final: 0.7061 (ptp) REVERT: B 437 SER cc_start: 0.9325 (m) cc_final: 0.9114 (p) REVERT: B 632 VAL cc_start: 0.8576 (m) cc_final: 0.7771 (m) REVERT: B 635 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8570 (mp0) outliers start: 4 outliers final: 1 residues processed: 408 average time/residue: 0.5414 time to fit residues: 346.0121 Evaluate side-chains 297 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 chunk 420 optimal weight: 7.9990 chunk 454 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS C 234 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 739 ASN D 377 HIS ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 37104 Z= 0.285 Angle : 0.726 14.191 50280 Z= 0.371 Chirality : 0.045 0.220 5724 Planarity : 0.006 0.070 6552 Dihedral : 6.582 60.025 5106 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.11 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.07 % 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: -2.37 (0.12), residues: 4626 helix: -0.43 (0.11), residues: 1989 sheet: -2.04 (0.21), residues: 527 loop : -2.60 (0.12), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 563 HIS 0.008 0.002 HIS A 666 PHE 0.018 0.002 PHE B 657 TYR 0.033 0.002 TYR A 224 ARG 0.011 0.001 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8217 (mtm180) REVERT: A 276 MET cc_start: 0.7462 (tpt) cc_final: 0.7145 (tpt) REVERT: A 633 MET cc_start: 0.8819 (mmm) cc_final: 0.8611 (mtm) REVERT: A 657 PHE cc_start: 0.6779 (p90) cc_final: 0.6458 (p90) REVERT: C 258 MET cc_start: -0.0353 (mmt) cc_final: -0.1043 (mmt) REVERT: C 545 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8414 (mmp80) REVERT: E 85 MET cc_start: 0.4458 (mmt) cc_final: 0.3514 (ttt) REVERT: E 237 LEU cc_start: 0.7665 (pt) cc_final: 0.7382 (pt) REVERT: E 258 MET cc_start: 0.5725 (mtt) cc_final: 0.4182 (mtt) REVERT: E 614 VAL cc_start: 0.7810 (t) cc_final: 0.7504 (t) REVERT: E 633 MET cc_start: 0.8481 (mmt) cc_final: 0.8074 (mmt) REVERT: E 683 MET cc_start: 0.8485 (mtt) cc_final: 0.7666 (mtt) REVERT: D 38 MET cc_start: 0.1667 (mmt) cc_final: 0.0979 (mtt) REVERT: D 139 HIS cc_start: 0.6608 (m90) cc_final: 0.6029 (m90) REVERT: D 226 LEU cc_start: 0.9005 (mm) cc_final: 0.8516 (tp) REVERT: D 258 MET cc_start: 0.2401 (mtt) cc_final: 0.1547 (mtt) REVERT: D 276 MET cc_start: 0.6070 (ttm) cc_final: 0.5530 (ttm) REVERT: D 602 TRP cc_start: 0.5779 (t-100) cc_final: 0.5111 (t-100) REVERT: F 2 ARG cc_start: 0.3659 (mmt90) cc_final: 0.3132 (mtp-110) REVERT: F 97 TYR cc_start: 0.7362 (p90) cc_final: 0.7041 (p90) REVERT: F 146 ARG cc_start: 0.6148 (ptp-170) cc_final: 0.5579 (tpt-90) REVERT: F 233 ILE cc_start: 0.8511 (mm) cc_final: 0.8032 (mm) REVERT: F 427 MET cc_start: 0.5390 (tpp) cc_final: 0.4505 (mmm) REVERT: F 625 LEU cc_start: 0.8541 (pt) cc_final: 0.8045 (mp) REVERT: F 702 MET cc_start: 0.6886 (ptp) cc_final: 0.6096 (pmm) REVERT: B 424 ILE cc_start: 0.8590 (mp) cc_final: 0.8348 (mp) REVERT: B 427 MET cc_start: 0.7641 (ptp) cc_final: 0.7295 (ptp) REVERT: B 437 SER cc_start: 0.9293 (m) cc_final: 0.9085 (p) REVERT: B 602 TRP cc_start: 0.4865 (p-90) cc_final: 0.4117 (p-90) REVERT: B 632 VAL cc_start: 0.8578 (m) cc_final: 0.7905 (m) REVERT: B 674 LYS cc_start: 0.3762 (ttpt) cc_final: 0.2557 (ttpt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.5456 time to fit residues: 304.2547 Evaluate side-chains 277 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 282 optimal weight: 0.0980 chunk 421 optimal weight: 10.0000 chunk 446 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 399 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 GLN ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN F 454 HIS ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 37104 Z= 0.273 Angle : 0.707 12.399 50280 Z= 0.360 Chirality : 0.045 0.283 5724 Planarity : 0.006 0.075 6552 Dihedral : 6.356 56.874 5106 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.06 % Favored : 91.85 % Rotamer: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.05 % 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: -2.11 (0.12), residues: 4626 helix: -0.12 (0.12), residues: 1976 sheet: -2.03 (0.21), residues: 533 loop : -2.51 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 602 HIS 0.010 0.002 HIS A 407 PHE 0.019 0.002 PHE B 657 TYR 0.035 0.002 TYR A 224 ARG 0.009 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8217 (mtm180) REVERT: A 276 MET cc_start: 0.7470 (tpt) cc_final: 0.7035 (tpt) REVERT: A 370 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7326 (ttt-90) REVERT: A 633 MET cc_start: 0.8768 (mmm) cc_final: 0.8246 (mtm) REVERT: A 657 PHE cc_start: 0.6759 (p90) cc_final: 0.6419 (p90) REVERT: C 160 MET cc_start: -0.1098 (mpp) cc_final: -0.2386 (ppp) REVERT: C 258 MET cc_start: 0.0124 (mmt) cc_final: -0.0883 (mmt) REVERT: C 545 ARG cc_start: 0.8702 (mtm180) cc_final: 0.8458 (mmp80) REVERT: C 567 ARG cc_start: 0.5352 (mmm-85) cc_final: 0.5083 (mpp80) REVERT: C 633 MET cc_start: 0.8617 (mpp) cc_final: 0.8385 (mmt) REVERT: E 85 MET cc_start: 0.4581 (mmt) cc_final: 0.3703 (ttt) REVERT: E 258 MET cc_start: 0.5805 (mtt) cc_final: 0.4070 (mtt) REVERT: E 633 MET cc_start: 0.8546 (mmt) cc_final: 0.8015 (mmt) REVERT: E 683 MET cc_start: 0.8646 (mtt) cc_final: 0.7601 (mtt) REVERT: D 38 MET cc_start: 0.1747 (mmt) cc_final: 0.0940 (mtt) REVERT: D 258 MET cc_start: 0.2399 (mtt) cc_final: 0.1556 (mtt) REVERT: D 276 MET cc_start: 0.6372 (ttm) cc_final: 0.5922 (ttm) REVERT: D 675 ASP cc_start: 0.8597 (m-30) cc_final: 0.7842 (p0) REVERT: F 97 TYR cc_start: 0.7384 (p90) cc_final: 0.7056 (p90) REVERT: F 233 ILE cc_start: 0.8167 (mm) cc_final: 0.7862 (mm) REVERT: F 309 ASN cc_start: 0.8859 (m-40) cc_final: 0.8582 (m-40) REVERT: F 427 MET cc_start: 0.5543 (tpp) cc_final: 0.4673 (mmm) REVERT: F 475 GLN cc_start: 0.8452 (mt0) cc_final: 0.8191 (mp10) REVERT: F 625 LEU cc_start: 0.8467 (pt) cc_final: 0.7885 (mp) REVERT: F 702 MET cc_start: 0.6824 (ptp) cc_final: 0.6015 (pmm) REVERT: B 422 ASP cc_start: 0.8749 (m-30) cc_final: 0.8538 (m-30) REVERT: B 437 SER cc_start: 0.9279 (m) cc_final: 0.9073 (p) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.5566 time to fit residues: 298.0188 Evaluate side-chains 269 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.8980 chunk 253 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 0.0670 chunk 184 optimal weight: 0.9980 chunk 381 optimal weight: 10.0000 chunk 308 optimal weight: 70.0000 chunk 0 optimal weight: 100.0000 chunk 228 optimal weight: 9.9990 chunk 400 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 overall best weight: 4.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 37104 Z= 0.229 Angle : 0.664 11.222 50280 Z= 0.339 Chirality : 0.044 0.175 5724 Planarity : 0.005 0.069 6552 Dihedral : 6.093 54.864 5106 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4626 helix: 0.13 (0.12), residues: 1990 sheet: -1.97 (0.21), residues: 525 loop : -2.43 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 298 HIS 0.009 0.001 HIS A 407 PHE 0.015 0.001 PHE B 657 TYR 0.026 0.002 TYR B 768 ARG 0.007 0.000 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7294 (tpt) cc_final: 0.6661 (tpt) REVERT: A 370 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7093 (ttt-90) REVERT: A 633 MET cc_start: 0.8805 (mmm) cc_final: 0.8362 (mpp) REVERT: A 657 PHE cc_start: 0.6738 (p90) cc_final: 0.6056 (p90) REVERT: C 160 MET cc_start: -0.1128 (mpp) cc_final: -0.2358 (ppp) REVERT: C 258 MET cc_start: -0.0038 (mmt) cc_final: -0.0989 (mmt) REVERT: C 545 ARG cc_start: 0.8713 (mtm180) cc_final: 0.8429 (mmp80) REVERT: E 85 MET cc_start: 0.4740 (mmt) cc_final: 0.3834 (ttt) REVERT: E 258 MET cc_start: 0.5556 (mtt) cc_final: 0.3871 (mtt) REVERT: E 409 MET cc_start: 0.7890 (tpt) cc_final: 0.7365 (tpt) REVERT: E 633 MET cc_start: 0.8499 (mmt) cc_final: 0.7977 (mmt) REVERT: E 683 MET cc_start: 0.8722 (mtt) cc_final: 0.7833 (mtt) REVERT: D 38 MET cc_start: 0.1769 (mmt) cc_final: 0.0944 (mtt) REVERT: D 217 MET cc_start: 0.8571 (mtt) cc_final: 0.8215 (ppp) REVERT: D 230 MET cc_start: 0.4313 (ttt) cc_final: 0.3910 (ttm) REVERT: D 258 MET cc_start: 0.2225 (mtt) cc_final: 0.1272 (mtt) REVERT: D 276 MET cc_start: 0.6467 (ttm) cc_final: 0.6101 (ttt) REVERT: D 439 MET cc_start: 0.8643 (mmm) cc_final: 0.8442 (mmt) REVERT: D 483 ASP cc_start: 0.7203 (p0) cc_final: 0.6911 (p0) REVERT: D 485 MET cc_start: 0.6617 (mmm) cc_final: 0.6311 (mmm) REVERT: D 675 ASP cc_start: 0.8593 (m-30) cc_final: 0.7838 (p0) REVERT: F 97 TYR cc_start: 0.7417 (p90) cc_final: 0.7108 (p90) REVERT: F 309 ASN cc_start: 0.8805 (m-40) cc_final: 0.8505 (m110) REVERT: F 475 GLN cc_start: 0.8438 (mt0) cc_final: 0.8151 (mp10) REVERT: F 485 MET cc_start: 0.5387 (mmp) cc_final: 0.4804 (tpp) REVERT: F 625 LEU cc_start: 0.8407 (pt) cc_final: 0.7779 (mp) REVERT: F 702 MET cc_start: 0.6851 (ptp) cc_final: 0.5965 (pmm) REVERT: B 385 ARG cc_start: 0.9209 (mtp180) cc_final: 0.8986 (mtm110) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5231 time to fit residues: 282.9253 Evaluate side-chains 268 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 5.9990 chunk 402 optimal weight: 40.0000 chunk 88 optimal weight: 50.0000 chunk 262 optimal weight: 20.0000 chunk 110 optimal weight: 0.0050 chunk 447 optimal weight: 7.9990 chunk 371 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 234 optimal weight: 50.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 138 ASN A 337 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 37104 Z= 0.238 Angle : 0.674 11.982 50280 Z= 0.343 Chirality : 0.044 0.172 5724 Planarity : 0.005 0.071 6552 Dihedral : 6.005 53.414 5106 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.47 % Favored : 91.48 % Rotamer: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4626 helix: 0.20 (0.12), residues: 2007 sheet: -1.86 (0.22), residues: 506 loop : -2.39 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 431 HIS 0.007 0.001 HIS A 407 PHE 0.016 0.001 PHE B 657 TYR 0.028 0.002 TYR A 224 ARG 0.011 0.000 ARG E 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7146 (tpt) cc_final: 0.6517 (tpt) REVERT: A 370 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7187 (ttt-90) REVERT: A 496 MET cc_start: 0.8669 (mpp) cc_final: 0.8466 (mpp) REVERT: A 516 MET cc_start: 0.4632 (tmm) cc_final: 0.3511 (tmm) REVERT: A 633 MET cc_start: 0.8793 (mmm) cc_final: 0.8269 (mtm) REVERT: C 160 MET cc_start: -0.1467 (mpp) cc_final: -0.2513 (ppp) REVERT: C 258 MET cc_start: -0.0297 (mmt) cc_final: -0.1311 (mmt) REVERT: C 427 MET cc_start: 0.8324 (tpt) cc_final: 0.7951 (tpt) REVERT: C 545 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8458 (mmp80) REVERT: C 633 MET cc_start: 0.8648 (mpp) cc_final: 0.8390 (mmt) REVERT: E 85 MET cc_start: 0.4697 (mmt) cc_final: 0.3799 (ttt) REVERT: E 258 MET cc_start: 0.5624 (mtt) cc_final: 0.3931 (mtt) REVERT: E 633 MET cc_start: 0.8550 (mmt) cc_final: 0.7991 (mmt) REVERT: E 683 MET cc_start: 0.8750 (mtt) cc_final: 0.7856 (mtt) REVERT: D 38 MET cc_start: 0.1761 (mmt) cc_final: 0.0936 (mtt) REVERT: D 217 MET cc_start: 0.8537 (mtt) cc_final: 0.8196 (ppp) REVERT: D 276 MET cc_start: 0.6512 (ttm) cc_final: 0.6088 (ttm) REVERT: D 483 ASP cc_start: 0.7099 (p0) cc_final: 0.6846 (p0) REVERT: D 485 MET cc_start: 0.6689 (mmm) cc_final: 0.6489 (mmm) REVERT: D 675 ASP cc_start: 0.8537 (m-30) cc_final: 0.7836 (p0) REVERT: D 713 MET cc_start: 0.7968 (mpp) cc_final: 0.7754 (mpp) REVERT: F 97 TYR cc_start: 0.7425 (p90) cc_final: 0.7134 (p90) REVERT: F 233 ILE cc_start: 0.7858 (mm) cc_final: 0.7486 (mm) REVERT: F 309 ASN cc_start: 0.8805 (m-40) cc_final: 0.8506 (m110) REVERT: F 427 MET cc_start: 0.5502 (tpt) cc_final: 0.5104 (tpt) REVERT: F 475 GLN cc_start: 0.8454 (mt0) cc_final: 0.8125 (mp10) REVERT: F 485 MET cc_start: 0.5356 (mmp) cc_final: 0.4950 (tpp) REVERT: F 625 LEU cc_start: 0.8430 (pt) cc_final: 0.7786 (mp) REVERT: F 702 MET cc_start: 0.6866 (ptp) cc_final: 0.6022 (pmm) REVERT: B 379 ILE cc_start: 0.9169 (tp) cc_final: 0.8931 (tp) REVERT: B 424 ILE cc_start: 0.8578 (mp) cc_final: 0.8343 (mp) REVERT: B 632 VAL cc_start: 0.8522 (m) cc_final: 0.8286 (m) outliers start: 1 outliers final: 1 residues processed: 329 average time/residue: 0.5178 time to fit residues: 274.0303 Evaluate side-chains 271 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 254 optimal weight: 30.0000 chunk 326 optimal weight: 30.0000 chunk 252 optimal weight: 30.0000 chunk 376 optimal weight: 7.9990 chunk 249 optimal weight: 40.0000 chunk 445 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS A 659 ASN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN E 407 HIS ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 649 GLN E 726 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 37104 Z= 0.383 Angle : 0.835 15.221 50280 Z= 0.422 Chirality : 0.048 0.256 5724 Planarity : 0.006 0.080 6552 Dihedral : 6.489 55.298 5106 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.35 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.09 % 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: -2.20 (0.12), residues: 4626 helix: -0.23 (0.11), residues: 2002 sheet: -2.16 (0.22), residues: 483 loop : -2.52 (0.12), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 602 HIS 0.014 0.002 HIS B 666 PHE 0.046 0.002 PHE B 203 TYR 0.042 0.003 TYR B 493 ARG 0.014 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7056 (tpt) cc_final: 0.6580 (tpt) REVERT: A 496 MET cc_start: 0.8754 (mpp) cc_final: 0.8470 (mpp) REVERT: A 516 MET cc_start: 0.4514 (tmm) cc_final: 0.3566 (tmm) REVERT: A 633 MET cc_start: 0.8949 (mmm) cc_final: 0.8544 (mpp) REVERT: C 160 MET cc_start: -0.1500 (mpp) cc_final: -0.2453 (ppp) REVERT: C 258 MET cc_start: 0.0211 (mmt) cc_final: -0.0937 (mmt) REVERT: C 427 MET cc_start: 0.8468 (tpt) cc_final: 0.8193 (tpt) REVERT: C 545 ARG cc_start: 0.8770 (mtm180) cc_final: 0.8502 (mmp80) REVERT: E 75 MET cc_start: 0.2968 (pmm) cc_final: 0.2473 (pmm) REVERT: E 85 MET cc_start: 0.4707 (mmt) cc_final: 0.3864 (ttt) REVERT: E 258 MET cc_start: 0.6283 (mtt) cc_final: 0.4498 (mtt) REVERT: E 331 GLU cc_start: 0.8514 (pm20) cc_final: 0.8171 (pm20) REVERT: E 409 MET cc_start: 0.7871 (tpt) cc_final: 0.7458 (tpt) REVERT: E 431 TRP cc_start: 0.5088 (t60) cc_final: 0.4860 (t60) REVERT: E 633 MET cc_start: 0.8705 (mmt) cc_final: 0.8109 (mmt) REVERT: E 683 MET cc_start: 0.8749 (mtt) cc_final: 0.7710 (mtt) REVERT: D 38 MET cc_start: 0.2108 (mmt) cc_final: 0.1283 (mtt) REVERT: D 258 MET cc_start: 0.2871 (mtt) cc_final: 0.2233 (mtt) REVERT: D 276 MET cc_start: 0.6701 (ttm) cc_final: 0.6369 (ttm) REVERT: D 483 ASP cc_start: 0.7013 (p0) cc_final: 0.6733 (p0) REVERT: D 675 ASP cc_start: 0.8670 (m-30) cc_final: 0.8035 (p0) REVERT: F 97 TYR cc_start: 0.7364 (p90) cc_final: 0.7089 (p90) REVERT: F 233 ILE cc_start: 0.8048 (mm) cc_final: 0.7664 (mm) REVERT: F 427 MET cc_start: 0.5826 (tpt) cc_final: 0.5320 (tpt) REVERT: F 475 GLN cc_start: 0.8502 (mt0) cc_final: 0.8146 (mp10) REVERT: F 702 MET cc_start: 0.6640 (ptp) cc_final: 0.5877 (pmm) REVERT: B 422 ASP cc_start: 0.8737 (m-30) cc_final: 0.8475 (m-30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5088 time to fit residues: 253.0204 Evaluate side-chains 247 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 350 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 37104 Z= 0.271 Angle : 0.726 14.064 50280 Z= 0.367 Chirality : 0.046 0.205 5724 Planarity : 0.006 0.073 6552 Dihedral : 6.259 54.227 5106 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.56 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.12), residues: 4626 helix: -0.00 (0.12), residues: 1995 sheet: -2.05 (0.22), residues: 484 loop : -2.45 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 602 HIS 0.015 0.002 HIS E 319 PHE 0.026 0.002 PHE B 203 TYR 0.026 0.002 TYR A 224 ARG 0.009 0.001 ARG C 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6913 (tpt) cc_final: 0.6317 (tpt) REVERT: A 372 MET cc_start: 0.8177 (tpp) cc_final: 0.7931 (tpp) REVERT: A 496 MET cc_start: 0.8728 (mpp) cc_final: 0.8498 (mpp) REVERT: A 516 MET cc_start: 0.4374 (tmm) cc_final: 0.3585 (tmm) REVERT: A 633 MET cc_start: 0.8935 (mmm) cc_final: 0.8536 (mpp) REVERT: C 160 MET cc_start: -0.1546 (mpp) cc_final: -0.2537 (ppp) REVERT: C 258 MET cc_start: 0.0086 (mmt) cc_final: -0.1066 (mmt) REVERT: C 427 MET cc_start: 0.8539 (tpt) cc_final: 0.8281 (tpt) REVERT: C 545 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8464 (mmp80) REVERT: E 85 MET cc_start: 0.4634 (mmt) cc_final: 0.3892 (ttt) REVERT: E 258 MET cc_start: 0.6012 (mtt) cc_final: 0.4218 (mtt) REVERT: E 331 GLU cc_start: 0.8378 (pm20) cc_final: 0.7964 (pm20) REVERT: E 427 MET cc_start: 0.8435 (tmm) cc_final: 0.8133 (tmm) REVERT: E 431 TRP cc_start: 0.4456 (t60) cc_final: 0.4224 (t60) REVERT: E 633 MET cc_start: 0.8655 (mmt) cc_final: 0.7954 (mmt) REVERT: E 683 MET cc_start: 0.8804 (mtt) cc_final: 0.7745 (mtt) REVERT: D 38 MET cc_start: 0.1997 (mmt) cc_final: 0.1189 (mtt) REVERT: D 258 MET cc_start: 0.2621 (mtt) cc_final: 0.1718 (mtt) REVERT: D 276 MET cc_start: 0.6606 (ttm) cc_final: 0.6264 (ttt) REVERT: D 439 MET cc_start: 0.8655 (mmm) cc_final: 0.8438 (mmt) REVERT: D 483 ASP cc_start: 0.7336 (p0) cc_final: 0.6842 (p0) REVERT: D 602 TRP cc_start: 0.6101 (t-100) cc_final: 0.5241 (t-100) REVERT: D 675 ASP cc_start: 0.8601 (m-30) cc_final: 0.7893 (p0) REVERT: F 97 TYR cc_start: 0.7335 (p90) cc_final: 0.7047 (p90) REVERT: F 229 GLN cc_start: 0.8137 (mp10) cc_final: 0.7923 (tp-100) REVERT: F 309 ASN cc_start: 0.8910 (m-40) cc_final: 0.8343 (m-40) REVERT: F 427 MET cc_start: 0.5478 (tpt) cc_final: 0.3591 (tpp) REVERT: F 642 THR cc_start: 0.8807 (m) cc_final: 0.8538 (m) REVERT: F 702 MET cc_start: 0.7004 (ptp) cc_final: 0.6229 (pmm) REVERT: B 222 ARG cc_start: 0.4242 (tpm170) cc_final: 0.3994 (tpm170) REVERT: B 379 ILE cc_start: 0.9210 (tp) cc_final: 0.8977 (tp) REVERT: B 431 TRP cc_start: 0.7431 (p-90) cc_final: 0.7217 (p-90) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4969 time to fit residues: 256.3438 Evaluate side-chains 256 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 389 optimal weight: 6.9990 chunk 414 optimal weight: 2.9990 chunk 249 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 325 optimal weight: 50.0000 chunk 127 optimal weight: 10.0000 chunk 374 optimal weight: 3.9990 chunk 392 optimal weight: 20.0000 chunk 413 optimal weight: 8.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 37104 Z= 0.317 Angle : 0.773 14.594 50280 Z= 0.391 Chirality : 0.047 0.209 5724 Planarity : 0.006 0.071 6552 Dihedral : 6.313 54.315 5106 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.46 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.11 % 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: -2.02 (0.12), residues: 4626 helix: -0.07 (0.12), residues: 1996 sheet: -2.02 (0.23), residues: 473 loop : -2.45 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 563 HIS 0.010 0.002 HIS E 319 PHE 0.025 0.002 PHE B 203 TYR 0.028 0.002 TYR B 493 ARG 0.007 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6872 (tpt) cc_final: 0.6360 (tpt) REVERT: A 372 MET cc_start: 0.8156 (tpp) cc_final: 0.7909 (tpp) REVERT: A 496 MET cc_start: 0.8756 (mpp) cc_final: 0.8456 (mpp) REVERT: A 516 MET cc_start: 0.4387 (tmm) cc_final: 0.3635 (tmm) REVERT: A 633 MET cc_start: 0.9035 (mmm) cc_final: 0.8660 (mpp) REVERT: A 683 MET cc_start: 0.8988 (mtt) cc_final: 0.8731 (mtm) REVERT: C 160 MET cc_start: -0.1496 (mpp) cc_final: -0.2447 (ppp) REVERT: C 258 MET cc_start: -0.0045 (mmt) cc_final: -0.1189 (mmt) REVERT: C 427 MET cc_start: 0.8558 (tpt) cc_final: 0.8311 (tpt) REVERT: C 545 ARG cc_start: 0.8744 (mtm180) cc_final: 0.8539 (mmp80) REVERT: C 633 MET cc_start: 0.8668 (mpp) cc_final: 0.8390 (mmt) REVERT: E 85 MET cc_start: 0.4792 (mmt) cc_final: 0.3966 (ttt) REVERT: E 217 MET cc_start: 0.7064 (tpt) cc_final: 0.6680 (mmt) REVERT: E 258 MET cc_start: 0.6092 (mtt) cc_final: 0.4298 (mtt) REVERT: E 331 GLU cc_start: 0.8373 (pm20) cc_final: 0.7971 (pm20) REVERT: E 409 MET cc_start: 0.7960 (tpt) cc_final: 0.7613 (tpt) REVERT: E 427 MET cc_start: 0.8292 (tmm) cc_final: 0.7987 (tmm) REVERT: E 633 MET cc_start: 0.8676 (mmt) cc_final: 0.7898 (mmt) REVERT: E 683 MET cc_start: 0.8790 (mtt) cc_final: 0.7687 (mtt) REVERT: D 38 MET cc_start: 0.2205 (mmt) cc_final: 0.1376 (mtt) REVERT: D 258 MET cc_start: 0.2769 (mtt) cc_final: 0.1665 (mtt) REVERT: D 276 MET cc_start: 0.6718 (ttm) cc_final: 0.6395 (ttt) REVERT: D 439 MET cc_start: 0.8731 (mmm) cc_final: 0.8482 (mmt) REVERT: D 602 TRP cc_start: 0.6215 (t-100) cc_final: 0.5291 (t-100) REVERT: D 675 ASP cc_start: 0.8620 (m-30) cc_final: 0.7910 (p0) REVERT: F 233 ILE cc_start: 0.7943 (mm) cc_final: 0.7569 (mm) REVERT: F 309 ASN cc_start: 0.8798 (m-40) cc_final: 0.8565 (m-40) REVERT: F 427 MET cc_start: 0.5632 (tpt) cc_final: 0.4336 (tpt) REVERT: F 475 GLN cc_start: 0.8493 (mt0) cc_final: 0.8148 (mp10) REVERT: F 702 MET cc_start: 0.6885 (ptp) cc_final: 0.6104 (pmm) REVERT: B 409 MET cc_start: 0.9100 (mmm) cc_final: 0.8544 (mpp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.5023 time to fit residues: 245.5061 Evaluate side-chains 251 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 8.9990 chunk 438 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 460 optimal weight: 1.9990 chunk 423 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 38 optimal weight: 0.2980 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 HIS F 138 ASN ** F 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37104 Z= 0.203 Angle : 0.670 13.483 50280 Z= 0.338 Chirality : 0.045 0.187 5724 Planarity : 0.005 0.078 6552 Dihedral : 5.965 52.483 5106 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.96 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4626 helix: 0.33 (0.12), residues: 1988 sheet: -1.87 (0.22), residues: 525 loop : -2.28 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 563 HIS 0.010 0.001 HIS E 319 PHE 0.020 0.001 PHE B 203 TYR 0.024 0.002 TYR A 224 ARG 0.008 0.000 ARG E 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6951 (tpt) cc_final: 0.6347 (tpt) REVERT: A 372 MET cc_start: 0.8209 (tpp) cc_final: 0.7995 (tpp) REVERT: A 496 MET cc_start: 0.8715 (mpp) cc_final: 0.8465 (mpp) REVERT: A 516 MET cc_start: 0.4508 (tmm) cc_final: 0.3887 (tmm) REVERT: A 633 MET cc_start: 0.8989 (mmm) cc_final: 0.8620 (mtm) REVERT: A 683 MET cc_start: 0.8970 (mtt) cc_final: 0.8743 (mtt) REVERT: C 160 MET cc_start: -0.1554 (mpp) cc_final: -0.2539 (ppp) REVERT: C 258 MET cc_start: -0.0367 (mmt) cc_final: -0.1365 (mmt) REVERT: C 427 MET cc_start: 0.8566 (tpt) cc_final: 0.8336 (tpt) REVERT: C 545 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8454 (mmp80) REVERT: C 633 MET cc_start: 0.8552 (mpp) cc_final: 0.8307 (mmt) REVERT: C 713 MET cc_start: 0.8718 (mmm) cc_final: 0.8517 (mmm) REVERT: E 85 MET cc_start: 0.4734 (mmt) cc_final: 0.3931 (ttt) REVERT: E 258 MET cc_start: 0.5777 (mtt) cc_final: 0.4025 (mtt) REVERT: E 331 GLU cc_start: 0.8291 (pm20) cc_final: 0.7908 (pm20) REVERT: E 385 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8567 (ptp-110) REVERT: E 633 MET cc_start: 0.8602 (mmt) cc_final: 0.7862 (mmt) REVERT: E 683 MET cc_start: 0.8795 (mtt) cc_final: 0.7784 (mtt) REVERT: D 38 MET cc_start: 0.1914 (mmt) cc_final: 0.1043 (mtt) REVERT: D 276 MET cc_start: 0.6566 (ttm) cc_final: 0.6255 (ttt) REVERT: D 439 MET cc_start: 0.8709 (mmm) cc_final: 0.8504 (mmt) REVERT: D 675 ASP cc_start: 0.8517 (m-30) cc_final: 0.7782 (p0) REVERT: F 97 TYR cc_start: 0.7399 (p90) cc_final: 0.7055 (p90) REVERT: F 229 GLN cc_start: 0.8259 (mp10) cc_final: 0.8028 (tp40) REVERT: F 309 ASN cc_start: 0.8696 (m-40) cc_final: 0.8448 (m110) REVERT: F 427 MET cc_start: 0.5450 (tpt) cc_final: 0.3706 (tpp) REVERT: B 228 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8129 (pt0) REVERT: B 379 ILE cc_start: 0.9279 (tp) cc_final: 0.8982 (tp) REVERT: B 409 MET cc_start: 0.9051 (mmm) cc_final: 0.8476 (mpp) REVERT: B 422 ASP cc_start: 0.8642 (m-30) cc_final: 0.8353 (m-30) REVERT: B 431 TRP cc_start: 0.7458 (p-90) cc_final: 0.7250 (p-90) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.5167 time to fit residues: 267.7519 Evaluate side-chains 264 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 8.9990 chunk 390 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 367 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 376 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN F 138 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.135256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.091587 restraints weight = 136623.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.087136 restraints weight = 142380.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.086280 restraints weight = 131702.182| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37104 Z= 0.178 Angle : 0.641 12.323 50280 Z= 0.323 Chirality : 0.044 0.193 5724 Planarity : 0.005 0.058 6552 Dihedral : 5.655 50.801 5106 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.12), residues: 4626 helix: 0.53 (0.12), residues: 2005 sheet: -1.67 (0.22), residues: 541 loop : -2.21 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.009 0.001 HIS E 319 PHE 0.019 0.001 PHE B 203 TYR 0.023 0.001 TYR A 224 ARG 0.035 0.000 ARG E 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7788.28 seconds wall clock time: 142 minutes 20.83 seconds (8540.83 seconds total)