Starting phenix.real_space_refine on Sun Mar 24 16:40:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp8_40676/03_2024/8sp8_40676_trim.pdb" } resolution = 2.79 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= 0.004 sd= 0.045 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 12 5.49 5 S 160 5.16 5 Cl 1 4.86 5 C 13920 2.51 5 N 3336 2.21 5 O 3652 1.98 5 H 19860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 492": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 594": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 628": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 492": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 594": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 628": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 492": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 594": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 628": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 492": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 594": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 628": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 360 Unusual residues: {' CA': 1, ' CL': 1, 'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 18.37, per 1000 atoms: 0.45 Number of scatterers: 40942 At special positions: 0 Unit cell: (149.325, 149.325, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 160 16.00 P 12 15.00 O 3652 8.00 N 3336 7.00 C 13920 6.00 H 19860 1.00 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: 33.00 Conformation dependent library (CDL) restraints added in 3.9 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 63.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.504A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.708A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.857A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.598A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.055A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.584A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.528A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.627A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.723A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP A 489 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 490 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 512 removed outlier: 3.530A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.809A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY A 624 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.797A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.652A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.792A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.707A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.858A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.599A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.055A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.585A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.529A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.673A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.627A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.722A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP B 489 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 490 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 removed outlier: 3.529A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.808A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.810A pdb=" N GLY B 624 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.707A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.859A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.598A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.054A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.585A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.528A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.626A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.722A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP C 489 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 490 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 512 removed outlier: 3.530A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.809A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY C 624 " --> pdb=" O ARG C 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.554A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.822A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.708A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.858A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.599A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.054A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.584A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 Processing helix chain 'D' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.527A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.628A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 478 through 485 removed outlier: 3.723A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 removed outlier: 6.598A pdb=" N ASP D 489 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 490 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 3.529A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.808A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY D 624 " --> pdb=" O ARG D 621 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'D' and resid 353 through 354 892 hydrogen bonds defined for protein. 2508 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: 15.81 Time building geometry restraints manager: 34.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.25: 22721 1.25 - 1.67: 18407 1.67 - 2.09: 272 2.09 - 2.50: 4 2.50 - 2.92: 12 Bond restraints: 41416 Sorted by residual: bond pdb=" CB ASP A 638 " pdb=" HB2 ASP A 638 " ideal model delta sigma weight residual 0.970 2.923 -1.953 2.00e-02 2.50e+03 9.54e+03 bond pdb=" CB ASP C 638 " pdb=" HB2 ASP C 638 " ideal model delta sigma weight residual 0.970 2.915 -1.945 2.00e-02 2.50e+03 9.46e+03 bond pdb=" CB ASP B 638 " pdb=" HB2 ASP B 638 " ideal model delta sigma weight residual 0.970 2.911 -1.941 2.00e-02 2.50e+03 9.42e+03 bond pdb=" CB ASP D 638 " pdb=" HB2 ASP D 638 " ideal model delta sigma weight residual 0.970 2.910 -1.940 2.00e-02 2.50e+03 9.41e+03 bond pdb=" CB ASP D 638 " pdb=" HB3 ASP D 638 " ideal model delta sigma weight residual 0.970 2.809 -1.839 2.00e-02 2.50e+03 8.46e+03 ... (remaining 41411 not shown) Histogram of bond angle deviations from ideal: 80.04 - 91.60: 8 91.60 - 103.16: 315 103.16 - 114.73: 50854 114.73 - 126.29: 22488 126.29 - 137.85: 475 Bond angle restraints: 74140 Sorted by residual: angle pdb=" HB2 ASP A 638 " pdb=" CB ASP A 638 " pdb=" HB3 ASP A 638 " ideal model delta sigma weight residual 110.00 80.04 29.96 3.00e+00 1.11e-01 9.97e+01 angle pdb=" HB2 ASP C 638 " pdb=" CB ASP C 638 " pdb=" HB3 ASP C 638 " ideal model delta sigma weight residual 110.00 80.20 29.80 3.00e+00 1.11e-01 9.87e+01 angle pdb=" HB2 ASP B 638 " pdb=" CB ASP B 638 " pdb=" HB3 ASP B 638 " ideal model delta sigma weight residual 110.00 80.21 29.79 3.00e+00 1.11e-01 9.86e+01 angle pdb=" HB2 ASP D 638 " pdb=" CB ASP D 638 " pdb=" HB3 ASP D 638 " ideal model delta sigma weight residual 110.00 80.24 29.76 3.00e+00 1.11e-01 9.84e+01 angle pdb=" C ASP D 638 " pdb=" CA ASP D 638 " pdb=" HA ASP D 638 " ideal model delta sigma weight residual 109.00 88.36 20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 74135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 19860 32.09 - 64.18: 560 64.18 - 96.27: 44 96.27 - 128.35: 40 128.35 - 160.44: 4 Dihedral angle restraints: 20508 sinusoidal: 11960 harmonic: 8548 Sorted by residual: dihedral pdb=" CA GLY D 411 " pdb=" C GLY D 411 " pdb=" N VAL D 412 " pdb=" CA VAL D 412 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY B 411 " pdb=" C GLY B 411 " pdb=" N VAL B 412 " pdb=" CA VAL B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY C 411 " pdb=" C GLY C 411 " pdb=" N VAL C 412 " pdb=" CA VAL C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 20505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2848 0.091 - 0.181: 327 0.181 - 0.272: 33 0.272 - 0.362: 4 0.362 - 0.453: 8 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CG LEU C 475 " pdb=" CB LEU C 475 " pdb=" CD1 LEU C 475 " pdb=" CD2 LEU C 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CG LEU A 475 " pdb=" CB LEU A 475 " pdb=" CD1 LEU A 475 " pdb=" CD2 LEU A 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 3217 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 709 " -0.143 2.00e-02 2.50e+03 2.59e-01 6.73e+02 pdb=" C29 POV C 709 " 0.340 2.00e-02 2.50e+03 pdb="C210 POV C 709 " -0.337 2.00e-02 2.50e+03 pdb="C211 POV C 709 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 709 " -0.143 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV B 709 " 0.339 2.00e-02 2.50e+03 pdb="C210 POV B 709 " -0.336 2.00e-02 2.50e+03 pdb="C211 POV B 709 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 711 " 0.142 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV D 711 " -0.339 2.00e-02 2.50e+03 pdb="C210 POV D 711 " 0.336 2.00e-02 2.50e+03 pdb="C211 POV D 711 " -0.140 2.00e-02 2.50e+03 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3084 2.23 - 2.82: 89818 2.82 - 3.41: 104517 3.41 - 4.01: 146895 4.01 - 4.60: 230678 Nonbonded interactions: 574992 Sorted by model distance: nonbonded pdb="HH12 ARG A 470 " pdb=" OE1 GLN A 596 " model vdw 1.636 1.850 nonbonded pdb="HH12 ARG D 470 " pdb=" OE1 GLN D 596 " model vdw 1.636 1.850 nonbonded pdb="HH12 ARG C 470 " pdb=" OE1 GLN C 596 " model vdw 1.636 1.850 nonbonded pdb="HH12 ARG B 470 " pdb=" OE1 GLN B 596 " model vdw 1.636 1.850 nonbonded pdb="HH12 ARG B 355 " pdb=" OD2 ASP B 364 " model vdw 1.656 1.850 ... (remaining 574987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 638) selection = (chain 'B' and resid 27 through 638) selection = (chain 'C' and resid 27 through 638) selection = (chain 'D' and resid 27 through 638) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.590 Extract box with map and model: 6.210 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 125.520 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.150 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.014 0.176 21556 Z= 0.856 Angle : 1.173 21.550 29140 Z= 0.554 Chirality : 0.065 0.453 3220 Planarity : 0.012 0.259 3532 Dihedral : 16.364 160.443 9180 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.14), residues: 2440 helix: -3.54 (0.09), residues: 1384 sheet: -3.59 (0.37), residues: 124 loop : -2.27 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 629 HIS 0.010 0.002 HIS A 582 PHE 0.021 0.003 PHE D 537 TYR 0.022 0.003 TYR C 547 ARG 0.011 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 2.960 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: A 174 ASN cc_start: 0.7348 (t0) cc_final: 0.6874 (t0) REVERT: A 195 LEU cc_start: 0.7827 (mt) cc_final: 0.7620 (mt) REVERT: A 208 ASN cc_start: 0.8227 (t0) cc_final: 0.7993 (t0) REVERT: A 262 LYS cc_start: 0.8602 (tttm) cc_final: 0.7909 (ttpp) REVERT: A 300 LYS cc_start: 0.8439 (mttm) cc_final: 0.8237 (mttm) REVERT: A 306 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7485 (mt0) REVERT: A 318 SER cc_start: 0.8072 (t) cc_final: 0.7780 (m) REVERT: A 322 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7587 (mtpm) REVERT: A 328 TYR cc_start: 0.8453 (m-10) cc_final: 0.8226 (m-80) REVERT: A 554 MET cc_start: 0.8864 (tpt) cc_final: 0.8636 (tpt) REVERT: A 577 MET cc_start: 0.7129 (mtm) cc_final: 0.6832 (mtp) REVERT: A 628 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7455 (mtp180) REVERT: A 635 ASP cc_start: 0.7232 (t70) cc_final: 0.6802 (p0) REVERT: B 174 ASN cc_start: 0.7367 (t0) cc_final: 0.6988 (t0) REVERT: B 195 LEU cc_start: 0.8019 (mt) cc_final: 0.7801 (mt) REVERT: B 211 PHE cc_start: 0.8731 (m-10) cc_final: 0.8489 (m-10) REVERT: B 262 LYS cc_start: 0.8652 (tttm) cc_final: 0.7960 (ttpp) REVERT: B 306 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7539 (mt0) REVERT: B 318 SER cc_start: 0.8195 (t) cc_final: 0.7834 (m) REVERT: B 322 LYS cc_start: 0.7957 (tmmt) cc_final: 0.7606 (mtpm) REVERT: B 328 TYR cc_start: 0.8498 (m-10) cc_final: 0.8255 (m-10) REVERT: B 602 VAL cc_start: 0.7695 (t) cc_final: 0.7492 (m) REVERT: B 628 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7545 (mpp-170) REVERT: B 635 ASP cc_start: 0.7102 (t70) cc_final: 0.6790 (p0) REVERT: C 113 GLU cc_start: 0.8239 (tt0) cc_final: 0.8017 (tt0) REVERT: C 174 ASN cc_start: 0.7331 (t0) cc_final: 0.6922 (t0) REVERT: C 195 LEU cc_start: 0.7936 (mt) cc_final: 0.7720 (mt) REVERT: C 208 ASN cc_start: 0.8305 (t0) cc_final: 0.8083 (t0) REVERT: C 262 LYS cc_start: 0.8629 (tttm) cc_final: 0.7921 (ttpp) REVERT: C 300 LYS cc_start: 0.8434 (mttm) cc_final: 0.8225 (mttm) REVERT: C 306 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7489 (mt0) REVERT: C 318 SER cc_start: 0.8140 (t) cc_final: 0.7786 (m) REVERT: C 322 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7552 (mtpm) REVERT: C 328 TYR cc_start: 0.8512 (m-10) cc_final: 0.8251 (m-10) REVERT: C 577 MET cc_start: 0.7178 (mtm) cc_final: 0.6948 (mtp) REVERT: C 602 VAL cc_start: 0.7633 (t) cc_final: 0.7424 (m) REVERT: C 628 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7479 (mpp-170) REVERT: C 635 ASP cc_start: 0.7110 (t70) cc_final: 0.6750 (p0) REVERT: D 113 GLU cc_start: 0.8287 (tt0) cc_final: 0.7984 (tt0) REVERT: D 174 ASN cc_start: 0.7364 (t0) cc_final: 0.6959 (t0) REVERT: D 195 LEU cc_start: 0.7979 (mt) cc_final: 0.7745 (mt) REVERT: D 211 PHE cc_start: 0.8723 (m-10) cc_final: 0.8455 (m-10) REVERT: D 262 LYS cc_start: 0.8664 (tttm) cc_final: 0.7951 (ttpp) REVERT: D 300 LYS cc_start: 0.8412 (mttm) cc_final: 0.8208 (mttm) REVERT: D 303 GLU cc_start: 0.7602 (mp0) cc_final: 0.7137 (mp0) REVERT: D 306 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7493 (mt0) REVERT: D 318 SER cc_start: 0.8182 (t) cc_final: 0.7825 (m) REVERT: D 322 LYS cc_start: 0.7989 (tmmt) cc_final: 0.7591 (mtpm) REVERT: D 328 TYR cc_start: 0.8482 (m-10) cc_final: 0.8184 (m-10) REVERT: D 577 MET cc_start: 0.7162 (mtm) cc_final: 0.6944 (mtp) REVERT: D 602 VAL cc_start: 0.7595 (t) cc_final: 0.7388 (m) REVERT: D 628 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7506 (mpp-170) REVERT: D 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6735 (p0) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 2.8709 time to fit residues: 1748.7131 Evaluate side-chains 374 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 221 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 197 ASN A 357 ASN A 582 HIS B 118 GLN B 197 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 582 HIS C 118 GLN C 197 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 582 HIS D 31 GLN D 118 GLN D 197 ASN D 357 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21556 Z= 0.242 Angle : 0.741 13.182 29140 Z= 0.377 Chirality : 0.040 0.250 3220 Planarity : 0.006 0.054 3532 Dihedral : 18.334 159.871 4456 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.11 % Rotamer: Outliers : 1.60 % Allowed : 11.77 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.16), residues: 2440 helix: -1.86 (0.11), residues: 1420 sheet: -3.23 (0.38), residues: 124 loop : -1.71 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 629 HIS 0.006 0.001 HIS B 582 PHE 0.015 0.001 PHE B 493 TYR 0.013 0.002 TYR A 222 ARG 0.006 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 362 time to evaluate : 3.102 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: A 174 ASN cc_start: 0.7458 (t0) cc_final: 0.6986 (t0) REVERT: A 208 ASN cc_start: 0.8212 (t0) cc_final: 0.7917 (t0) REVERT: A 262 LYS cc_start: 0.8641 (tttm) cc_final: 0.7952 (ttpp) REVERT: A 300 LYS cc_start: 0.8404 (mttm) cc_final: 0.8183 (mttm) REVERT: A 303 GLU cc_start: 0.7453 (mp0) cc_final: 0.7015 (mp0) REVERT: A 318 SER cc_start: 0.7420 (t) cc_final: 0.6905 (m) REVERT: A 322 LYS cc_start: 0.7800 (tmmt) cc_final: 0.7450 (mtpm) REVERT: A 328 TYR cc_start: 0.8450 (m-10) cc_final: 0.8226 (m-80) REVERT: A 410 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6516 (mtp) REVERT: A 554 MET cc_start: 0.8926 (tpt) cc_final: 0.8314 (tpt) REVERT: A 596 GLN cc_start: 0.6644 (mt0) cc_final: 0.5940 (mm-40) REVERT: A 628 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7466 (mpp-170) REVERT: A 635 ASP cc_start: 0.7063 (t70) cc_final: 0.6574 (p0) REVERT: B 174 ASN cc_start: 0.7426 (t0) cc_final: 0.6903 (t0) REVERT: B 262 LYS cc_start: 0.8664 (tttm) cc_final: 0.8024 (ttpp) REVERT: B 314 LYS cc_start: 0.7386 (ttpt) cc_final: 0.6866 (ttmm) REVERT: B 318 SER cc_start: 0.7665 (t) cc_final: 0.7087 (m) REVERT: B 322 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7522 (mtpm) REVERT: B 328 TYR cc_start: 0.8477 (m-10) cc_final: 0.8220 (m-80) REVERT: B 596 GLN cc_start: 0.6705 (mt0) cc_final: 0.6073 (mm-40) REVERT: B 602 VAL cc_start: 0.7663 (t) cc_final: 0.7448 (m) REVERT: B 628 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7539 (mpp-170) REVERT: B 635 ASP cc_start: 0.7006 (t70) cc_final: 0.6690 (p0) REVERT: C 174 ASN cc_start: 0.7384 (t0) cc_final: 0.6896 (t0) REVERT: C 208 ASN cc_start: 0.8215 (t0) cc_final: 0.7971 (t0) REVERT: C 211 PHE cc_start: 0.8777 (m-10) cc_final: 0.8523 (m-10) REVERT: C 262 LYS cc_start: 0.8649 (tttm) cc_final: 0.7996 (ttpp) REVERT: C 314 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6618 (ttmm) REVERT: C 315 GLU cc_start: 0.8052 (mp0) cc_final: 0.7198 (mp0) REVERT: C 318 SER cc_start: 0.7548 (t) cc_final: 0.6994 (m) REVERT: C 322 LYS cc_start: 0.7785 (tmmt) cc_final: 0.7447 (mtpm) REVERT: C 328 TYR cc_start: 0.8485 (m-10) cc_final: 0.8220 (m-80) REVERT: C 554 MET cc_start: 0.8837 (tpt) cc_final: 0.8469 (tpt) REVERT: C 596 GLN cc_start: 0.6535 (mt0) cc_final: 0.5876 (mm-40) REVERT: C 602 VAL cc_start: 0.7579 (t) cc_final: 0.7378 (m) REVERT: C 628 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7475 (mpp-170) REVERT: C 635 ASP cc_start: 0.7007 (t70) cc_final: 0.6616 (p0) REVERT: D 113 GLU cc_start: 0.8301 (tt0) cc_final: 0.8082 (tt0) REVERT: D 174 ASN cc_start: 0.7347 (t0) cc_final: 0.6892 (t0) REVERT: D 262 LYS cc_start: 0.8672 (tttm) cc_final: 0.7937 (ttpp) REVERT: D 303 GLU cc_start: 0.7472 (mp0) cc_final: 0.7106 (mp0) REVERT: D 314 LYS cc_start: 0.7338 (ttpt) cc_final: 0.6806 (ttmm) REVERT: D 318 SER cc_start: 0.7548 (t) cc_final: 0.6989 (m) REVERT: D 322 LYS cc_start: 0.7819 (tmmt) cc_final: 0.7489 (mtpm) REVERT: D 328 TYR cc_start: 0.8483 (m-10) cc_final: 0.8169 (m-10) REVERT: D 410 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6507 (mtp) REVERT: D 554 MET cc_start: 0.8904 (tpt) cc_final: 0.8425 (tpt) REVERT: D 596 GLN cc_start: 0.6680 (mt0) cc_final: 0.6024 (mm-40) REVERT: D 628 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7507 (mpp-170) REVERT: D 635 ASP cc_start: 0.6984 (t70) cc_final: 0.6617 (p0) outliers start: 34 outliers final: 12 residues processed: 386 average time/residue: 2.4749 time to fit residues: 1101.8615 Evaluate side-chains 338 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 324 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.5980 chunk 239 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 91 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21556 Z= 0.368 Angle : 0.717 10.229 29140 Z= 0.352 Chirality : 0.043 0.234 3220 Planarity : 0.005 0.055 3532 Dihedral : 16.980 153.246 4456 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.07 % Allowed : 12.48 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 2440 helix: -0.93 (0.13), residues: 1476 sheet: -3.75 (0.48), residues: 84 loop : -1.49 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.005 0.001 HIS D 522 PHE 0.016 0.002 PHE D 493 TYR 0.014 0.002 TYR C 547 ARG 0.006 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 361 time to evaluate : 3.059 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: A 51 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 174 ASN cc_start: 0.7577 (t0) cc_final: 0.7138 (t0) REVERT: A 211 PHE cc_start: 0.8762 (m-10) cc_final: 0.8501 (m-10) REVERT: A 262 LYS cc_start: 0.8796 (tttm) cc_final: 0.8031 (ttpp) REVERT: A 300 LYS cc_start: 0.8429 (mttm) cc_final: 0.8215 (mttm) REVERT: A 303 GLU cc_start: 0.7579 (mp0) cc_final: 0.7090 (mp0) REVERT: A 314 LYS cc_start: 0.7298 (ttpt) cc_final: 0.6953 (ttmm) REVERT: A 322 LYS cc_start: 0.7828 (tmmt) cc_final: 0.7415 (mtpm) REVERT: A 332 LEU cc_start: 0.8364 (mt) cc_final: 0.8137 (mt) REVERT: A 596 GLN cc_start: 0.6759 (mt0) cc_final: 0.6028 (mm-40) REVERT: A 621 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7427 (ttp-110) REVERT: A 622 GLU cc_start: 0.7814 (pm20) cc_final: 0.7404 (pm20) REVERT: A 628 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7412 (mpp-170) REVERT: A 635 ASP cc_start: 0.7130 (t70) cc_final: 0.6633 (p0) REVERT: B 51 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 174 ASN cc_start: 0.7586 (t0) cc_final: 0.7143 (t0) REVERT: B 262 LYS cc_start: 0.8739 (tttm) cc_final: 0.7981 (ttpp) REVERT: B 314 LYS cc_start: 0.7379 (ttpt) cc_final: 0.7059 (ttmm) REVERT: B 322 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7468 (mtpm) REVERT: B 596 GLN cc_start: 0.6689 (mt0) cc_final: 0.6007 (mm-40) REVERT: B 602 VAL cc_start: 0.7802 (t) cc_final: 0.7528 (m) REVERT: B 628 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7542 (mpp-170) REVERT: B 635 ASP cc_start: 0.7110 (t70) cc_final: 0.6686 (p0) REVERT: C 51 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7610 (tt) REVERT: C 174 ASN cc_start: 0.7564 (t0) cc_final: 0.7087 (t0) REVERT: C 262 LYS cc_start: 0.8732 (tttm) cc_final: 0.7957 (ttpp) REVERT: C 314 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6986 (ttmm) REVERT: C 322 LYS cc_start: 0.7833 (tmmt) cc_final: 0.7408 (mtpm) REVERT: C 332 LEU cc_start: 0.8362 (mt) cc_final: 0.8150 (mt) REVERT: C 410 MET cc_start: 0.6865 (mtp) cc_final: 0.6565 (mtm) REVERT: C 596 GLN cc_start: 0.6663 (mt0) cc_final: 0.5950 (mm-40) REVERT: C 602 VAL cc_start: 0.7740 (t) cc_final: 0.7458 (m) REVERT: C 628 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7471 (mpp-170) REVERT: C 635 ASP cc_start: 0.7132 (t70) cc_final: 0.6607 (p0) REVERT: D 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7614 (tt) REVERT: D 113 GLU cc_start: 0.8321 (tt0) cc_final: 0.8098 (tt0) REVERT: D 174 ASN cc_start: 0.7382 (t0) cc_final: 0.7131 (t0) REVERT: D 262 LYS cc_start: 0.8739 (tttm) cc_final: 0.7968 (ttpp) REVERT: D 303 GLU cc_start: 0.7541 (mp0) cc_final: 0.7081 (mp0) REVERT: D 314 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7000 (ttmm) REVERT: D 322 LYS cc_start: 0.7849 (tmmt) cc_final: 0.7436 (mtpm) REVERT: D 332 LEU cc_start: 0.8355 (mt) cc_final: 0.8153 (mt) REVERT: D 410 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6373 (mtp) REVERT: D 492 ARG cc_start: 0.6192 (tpp80) cc_final: 0.5650 (tpp80) REVERT: D 596 GLN cc_start: 0.6661 (mt0) cc_final: 0.5937 (mm-40) REVERT: D 622 GLU cc_start: 0.7747 (pm20) cc_final: 0.7422 (pm20) REVERT: D 628 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7501 (mpp-170) REVERT: D 635 ASP cc_start: 0.7105 (t70) cc_final: 0.6633 (p0) outliers start: 44 outliers final: 26 residues processed: 387 average time/residue: 2.2570 time to fit residues: 1024.5844 Evaluate side-chains 348 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 317 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 357 ASN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21556 Z= 0.189 Angle : 0.619 8.057 29140 Z= 0.305 Chirality : 0.038 0.201 3220 Planarity : 0.004 0.055 3532 Dihedral : 15.707 152.163 4456 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 2.35 % Allowed : 14.60 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2440 helix: -0.15 (0.14), residues: 1436 sheet: -3.60 (0.48), residues: 84 loop : -1.22 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS C 201 PHE 0.019 0.001 PHE A 415 TYR 0.010 0.001 TYR A 222 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 325 time to evaluate : 3.207 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: A 51 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7674 (tt) REVERT: A 174 ASN cc_start: 0.7555 (t0) cc_final: 0.7104 (t0) REVERT: A 262 LYS cc_start: 0.8775 (tttm) cc_final: 0.8015 (ttpp) REVERT: A 300 LYS cc_start: 0.8413 (mttm) cc_final: 0.8207 (mttm) REVERT: A 303 GLU cc_start: 0.7607 (mp0) cc_final: 0.7099 (mp0) REVERT: A 314 LYS cc_start: 0.7221 (ttpt) cc_final: 0.6877 (ttmm) REVERT: A 322 LYS cc_start: 0.7795 (tmmt) cc_final: 0.7414 (mtpm) REVERT: A 596 GLN cc_start: 0.6667 (mt0) cc_final: 0.5960 (mm-40) REVERT: A 621 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7417 (ttp-110) REVERT: A 622 GLU cc_start: 0.7753 (pm20) cc_final: 0.7338 (pm20) REVERT: A 628 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7410 (mpp-170) REVERT: A 635 ASP cc_start: 0.7098 (t70) cc_final: 0.6704 (p0) REVERT: B 51 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7649 (tt) REVERT: B 174 ASN cc_start: 0.7598 (t0) cc_final: 0.7048 (t0) REVERT: B 262 LYS cc_start: 0.8790 (tttm) cc_final: 0.8033 (ttpp) REVERT: B 314 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6993 (ttmm) REVERT: B 322 LYS cc_start: 0.7815 (tmmt) cc_final: 0.7458 (mtpm) REVERT: B 410 MET cc_start: 0.6975 (mtp) cc_final: 0.6640 (mtm) REVERT: B 596 GLN cc_start: 0.6758 (mt0) cc_final: 0.6053 (mm-40) REVERT: B 602 VAL cc_start: 0.7832 (t) cc_final: 0.7549 (m) REVERT: B 628 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7500 (mpp-170) REVERT: B 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6701 (p0) REVERT: C 51 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7625 (tt) REVERT: C 174 ASN cc_start: 0.7507 (t0) cc_final: 0.7026 (t0) REVERT: C 262 LYS cc_start: 0.8791 (tttm) cc_final: 0.7981 (ttpp) REVERT: C 314 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6875 (ttmm) REVERT: C 322 LYS cc_start: 0.7751 (tmmt) cc_final: 0.7387 (mtpm) REVERT: C 410 MET cc_start: 0.6895 (mtp) cc_final: 0.6672 (mtm) REVERT: C 492 ARG cc_start: 0.6152 (tpp80) cc_final: 0.5518 (tpp80) REVERT: C 596 GLN cc_start: 0.6633 (mt0) cc_final: 0.5922 (mm-40) REVERT: C 602 VAL cc_start: 0.7813 (t) cc_final: 0.7523 (m) REVERT: C 628 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7434 (mpp-170) REVERT: C 635 ASP cc_start: 0.7079 (t70) cc_final: 0.6644 (p0) REVERT: D 51 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7630 (tt) REVERT: D 113 GLU cc_start: 0.8296 (tt0) cc_final: 0.8080 (tt0) REVERT: D 174 ASN cc_start: 0.7377 (t0) cc_final: 0.7043 (t0) REVERT: D 262 LYS cc_start: 0.8791 (tttm) cc_final: 0.8023 (ttpp) REVERT: D 301 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7837 (mtpm) REVERT: D 303 GLU cc_start: 0.7597 (mp0) cc_final: 0.7072 (mp0) REVERT: D 314 LYS cc_start: 0.7266 (ttpt) cc_final: 0.6937 (ttmm) REVERT: D 322 LYS cc_start: 0.7776 (tmmt) cc_final: 0.7421 (mtpm) REVERT: D 410 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6542 (mtp) REVERT: D 596 GLN cc_start: 0.6674 (mt0) cc_final: 0.5989 (mm-40) REVERT: D 621 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7330 (ttp-110) REVERT: D 622 GLU cc_start: 0.7756 (pm20) cc_final: 0.7412 (pm20) REVERT: D 628 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7460 (mpp-170) REVERT: D 635 ASP cc_start: 0.7085 (t70) cc_final: 0.6641 (p0) outliers start: 50 outliers final: 24 residues processed: 352 average time/residue: 2.3632 time to fit residues: 966.9820 Evaluate side-chains 333 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 357 ASN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21556 Z= 0.221 Angle : 0.595 6.845 29140 Z= 0.296 Chirality : 0.039 0.228 3220 Planarity : 0.004 0.057 3532 Dihedral : 14.850 146.508 4456 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.21 % Allowed : 15.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2440 helix: 0.24 (0.14), residues: 1452 sheet: -3.65 (0.48), residues: 84 loop : -1.08 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 PHE 0.015 0.001 PHE A 415 TYR 0.012 0.001 TYR D 216 ARG 0.005 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 331 time to evaluate : 3.416 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: A 51 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7600 (tt) REVERT: A 174 ASN cc_start: 0.7617 (t0) cc_final: 0.7116 (t0) REVERT: A 262 LYS cc_start: 0.8790 (tttm) cc_final: 0.8016 (ttpp) REVERT: A 300 LYS cc_start: 0.8416 (mttm) cc_final: 0.8213 (mttm) REVERT: A 303 GLU cc_start: 0.7629 (mp0) cc_final: 0.7065 (mp0) REVERT: A 314 LYS cc_start: 0.7315 (ttpt) cc_final: 0.6931 (ttmm) REVERT: A 322 LYS cc_start: 0.7779 (tmmt) cc_final: 0.7397 (mtpm) REVERT: A 596 GLN cc_start: 0.6738 (mt0) cc_final: 0.5997 (mm-40) REVERT: A 621 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7397 (ttp-110) REVERT: A 622 GLU cc_start: 0.7810 (pm20) cc_final: 0.7378 (pm20) REVERT: A 628 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7402 (mpp-170) REVERT: A 635 ASP cc_start: 0.7126 (t70) cc_final: 0.6726 (p0) REVERT: B 51 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7617 (tt) REVERT: B 174 ASN cc_start: 0.7588 (t0) cc_final: 0.7043 (t0) REVERT: B 262 LYS cc_start: 0.8768 (tttm) cc_final: 0.7949 (ttpp) REVERT: B 314 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6956 (ttmm) REVERT: B 322 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7431 (mtpm) REVERT: B 410 MET cc_start: 0.6917 (mtp) cc_final: 0.6712 (mtm) REVERT: B 596 GLN cc_start: 0.6803 (mt0) cc_final: 0.6049 (mm-40) REVERT: B 602 VAL cc_start: 0.7905 (t) cc_final: 0.7605 (m) REVERT: B 628 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7468 (mpp-170) REVERT: B 635 ASP cc_start: 0.7094 (t70) cc_final: 0.6744 (p0) REVERT: C 51 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7586 (tt) REVERT: C 174 ASN cc_start: 0.7526 (t0) cc_final: 0.7060 (t0) REVERT: C 262 LYS cc_start: 0.8758 (tttm) cc_final: 0.7919 (ttpp) REVERT: C 314 LYS cc_start: 0.7192 (ttpt) cc_final: 0.6845 (ttmm) REVERT: C 322 LYS cc_start: 0.7738 (tmmt) cc_final: 0.7367 (mtpm) REVERT: C 596 GLN cc_start: 0.6768 (mt0) cc_final: 0.6014 (mm-40) REVERT: C 602 VAL cc_start: 0.7841 (t) cc_final: 0.7550 (m) REVERT: C 628 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7414 (mpp-170) REVERT: C 635 ASP cc_start: 0.7101 (t70) cc_final: 0.6691 (p0) REVERT: D 51 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7621 (tt) REVERT: D 113 GLU cc_start: 0.8334 (tt0) cc_final: 0.8094 (tt0) REVERT: D 167 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7877 (tp) REVERT: D 174 ASN cc_start: 0.7526 (t0) cc_final: 0.7066 (t0) REVERT: D 262 LYS cc_start: 0.8803 (tttm) cc_final: 0.8078 (ttpp) REVERT: D 301 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7864 (mtpm) REVERT: D 303 GLU cc_start: 0.7627 (mp0) cc_final: 0.7047 (mp0) REVERT: D 314 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6891 (ttmm) REVERT: D 322 LYS cc_start: 0.7766 (tmmt) cc_final: 0.7397 (mtpm) REVERT: D 474 MET cc_start: 0.1895 (mmt) cc_final: 0.1691 (mtt) REVERT: D 596 GLN cc_start: 0.6634 (mt0) cc_final: 0.5959 (mm-40) REVERT: D 621 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7359 (ttp-110) REVERT: D 622 GLU cc_start: 0.7839 (pm20) cc_final: 0.7460 (pm20) REVERT: D 628 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7442 (mpp-170) REVERT: D 635 ASP cc_start: 0.7061 (t70) cc_final: 0.6675 (p0) outliers start: 47 outliers final: 30 residues processed: 361 average time/residue: 2.3470 time to fit residues: 988.3768 Evaluate side-chains 343 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 7.9990 chunk 212 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN A 357 ASN B 31 GLN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21556 Z= 0.302 Angle : 0.618 6.551 29140 Z= 0.306 Chirality : 0.040 0.221 3220 Planarity : 0.004 0.056 3532 Dihedral : 14.737 138.550 4456 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.54 % Allowed : 15.54 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2440 helix: 0.26 (0.14), residues: 1484 sheet: -2.77 (0.56), residues: 64 loop : -1.10 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.003 0.001 HIS A 426 PHE 0.015 0.001 PHE A 415 TYR 0.015 0.002 TYR D 216 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 320 time to evaluate : 3.312 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: A 51 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 174 ASN cc_start: 0.7533 (t0) cc_final: 0.7175 (t0) REVERT: A 262 LYS cc_start: 0.8770 (tttm) cc_final: 0.7989 (ttpp) REVERT: A 300 LYS cc_start: 0.8424 (mttm) cc_final: 0.8224 (mttm) REVERT: A 303 GLU cc_start: 0.7683 (mp0) cc_final: 0.7056 (mp0) REVERT: A 314 LYS cc_start: 0.7272 (ttpt) cc_final: 0.6875 (ttmm) REVERT: A 322 LYS cc_start: 0.7734 (tmmt) cc_final: 0.7368 (mtpm) REVERT: A 492 ARG cc_start: 0.6181 (tpp80) cc_final: 0.5665 (tpp80) REVERT: A 596 GLN cc_start: 0.6811 (mt0) cc_final: 0.6010 (mm-40) REVERT: A 622 GLU cc_start: 0.7848 (pm20) cc_final: 0.7349 (pm20) REVERT: A 628 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7369 (mpp-170) REVERT: A 635 ASP cc_start: 0.7120 (t70) cc_final: 0.6609 (p0) REVERT: B 51 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 167 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 174 ASN cc_start: 0.7645 (t0) cc_final: 0.7076 (t0) REVERT: B 262 LYS cc_start: 0.8780 (tttm) cc_final: 0.7967 (ttpp) REVERT: B 314 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6971 (ttmm) REVERT: B 322 LYS cc_start: 0.7808 (tmmt) cc_final: 0.7422 (mtpm) REVERT: B 596 GLN cc_start: 0.6821 (mt0) cc_final: 0.6056 (mm-40) REVERT: B 602 VAL cc_start: 0.7935 (t) cc_final: 0.7617 (m) REVERT: B 628 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7462 (mpp-170) REVERT: B 635 ASP cc_start: 0.7122 (t70) cc_final: 0.6676 (p0) REVERT: C 51 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7556 (tt) REVERT: C 167 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7841 (tp) REVERT: C 174 ASN cc_start: 0.7583 (t0) cc_final: 0.7131 (t0) REVERT: C 262 LYS cc_start: 0.8767 (tttm) cc_final: 0.7936 (ttpp) REVERT: C 314 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6887 (ttmm) REVERT: C 322 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7377 (mtpm) REVERT: C 596 GLN cc_start: 0.6824 (mt0) cc_final: 0.6023 (mm-40) REVERT: C 602 VAL cc_start: 0.7821 (t) cc_final: 0.7538 (m) REVERT: C 628 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7400 (mpp-170) REVERT: C 635 ASP cc_start: 0.7119 (t70) cc_final: 0.6609 (p0) REVERT: D 51 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7604 (tt) REVERT: D 113 GLU cc_start: 0.8319 (tt0) cc_final: 0.8083 (tt0) REVERT: D 167 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7882 (tp) REVERT: D 174 ASN cc_start: 0.7607 (t0) cc_final: 0.7150 (t0) REVERT: D 262 LYS cc_start: 0.8776 (tttm) cc_final: 0.7989 (ttpp) REVERT: D 301 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7840 (mtpm) REVERT: D 303 GLU cc_start: 0.7710 (mp0) cc_final: 0.7073 (mp0) REVERT: D 314 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6908 (ttmm) REVERT: D 322 LYS cc_start: 0.7770 (tmmt) cc_final: 0.7384 (mtpm) REVERT: D 596 GLN cc_start: 0.6656 (mt0) cc_final: 0.5954 (mm-40) REVERT: D 621 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7399 (ttp-110) REVERT: D 622 GLU cc_start: 0.7898 (pm20) cc_final: 0.7486 (pm20) REVERT: D 628 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7401 (mpp-170) REVERT: D 635 ASP cc_start: 0.7104 (t70) cc_final: 0.6622 (p0) outliers start: 54 outliers final: 28 residues processed: 351 average time/residue: 2.3282 time to fit residues: 955.6909 Evaluate side-chains 353 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 317 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21556 Z= 0.192 Angle : 0.571 6.074 29140 Z= 0.286 Chirality : 0.038 0.187 3220 Planarity : 0.004 0.055 3532 Dihedral : 13.980 133.397 4456 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer: Outliers : 2.31 % Allowed : 16.05 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2440 helix: 0.56 (0.14), residues: 1464 sheet: -2.67 (0.57), residues: 64 loop : -0.99 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS C 201 PHE 0.011 0.001 PHE A 415 TYR 0.012 0.001 TYR A 216 ARG 0.007 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 323 time to evaluate : 3.089 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: A 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7590 (tt) REVERT: A 174 ASN cc_start: 0.7530 (t0) cc_final: 0.6998 (t0) REVERT: A 262 LYS cc_start: 0.8757 (tttm) cc_final: 0.7966 (ttpp) REVERT: A 303 GLU cc_start: 0.7667 (mp0) cc_final: 0.7037 (mp0) REVERT: A 314 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6849 (ttmm) REVERT: A 322 LYS cc_start: 0.7747 (tmmt) cc_final: 0.7377 (mtpm) REVERT: A 492 ARG cc_start: 0.6180 (tpp80) cc_final: 0.5558 (tpp80) REVERT: A 596 GLN cc_start: 0.6775 (mt0) cc_final: 0.5937 (mm-40) REVERT: A 622 GLU cc_start: 0.7863 (pm20) cc_final: 0.7348 (pm20) REVERT: A 628 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7371 (mpp-170) REVERT: A 635 ASP cc_start: 0.7100 (t70) cc_final: 0.6659 (p0) REVERT: B 51 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7623 (tt) REVERT: B 153 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7936 (mtt90) REVERT: B 167 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 174 ASN cc_start: 0.7595 (t0) cc_final: 0.7040 (t0) REVERT: B 262 LYS cc_start: 0.8770 (tttm) cc_final: 0.7956 (ttpp) REVERT: B 314 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6947 (ttmm) REVERT: B 322 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7413 (mtpm) REVERT: B 596 GLN cc_start: 0.6825 (mt0) cc_final: 0.6008 (mm-40) REVERT: B 602 VAL cc_start: 0.7924 (t) cc_final: 0.7606 (m) REVERT: B 628 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7415 (mpp-170) REVERT: B 635 ASP cc_start: 0.7100 (t70) cc_final: 0.6730 (p0) REVERT: C 51 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7561 (tt) REVERT: C 167 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (tp) REVERT: C 174 ASN cc_start: 0.7524 (t0) cc_final: 0.7047 (t0) REVERT: C 262 LYS cc_start: 0.8764 (tttm) cc_final: 0.7957 (ttpp) REVERT: C 314 LYS cc_start: 0.7210 (ttpt) cc_final: 0.6860 (ttmm) REVERT: C 322 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7365 (mtpm) REVERT: C 596 GLN cc_start: 0.6736 (mt0) cc_final: 0.5958 (mm-40) REVERT: C 602 VAL cc_start: 0.7814 (t) cc_final: 0.7536 (m) REVERT: C 628 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7378 (mpp-170) REVERT: C 635 ASP cc_start: 0.7085 (t70) cc_final: 0.6670 (p0) REVERT: D 51 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7591 (tt) REVERT: D 113 GLU cc_start: 0.8297 (tt0) cc_final: 0.8070 (tt0) REVERT: D 167 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7894 (tp) REVERT: D 174 ASN cc_start: 0.7568 (t0) cc_final: 0.7101 (t0) REVERT: D 262 LYS cc_start: 0.8772 (tttm) cc_final: 0.7984 (ttpp) REVERT: D 303 GLU cc_start: 0.7714 (mp0) cc_final: 0.7109 (mp0) REVERT: D 314 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6882 (ttmm) REVERT: D 322 LYS cc_start: 0.7763 (tmmt) cc_final: 0.7382 (mtpm) REVERT: D 596 GLN cc_start: 0.6666 (mt0) cc_final: 0.5951 (mm-40) REVERT: D 621 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7383 (ttp-110) REVERT: D 622 GLU cc_start: 0.7899 (pm20) cc_final: 0.7548 (pm20) REVERT: D 628 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7403 (mpp-170) REVERT: D 635 ASP cc_start: 0.7073 (t70) cc_final: 0.6661 (p0) outliers start: 49 outliers final: 26 residues processed: 352 average time/residue: 2.3407 time to fit residues: 961.0129 Evaluate side-chains 351 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 317 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 357 ASN B 357 ASN C 31 GLN C 357 ASN D 357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21556 Z= 0.283 Angle : 0.593 6.455 29140 Z= 0.294 Chirality : 0.040 0.216 3220 Planarity : 0.004 0.055 3532 Dihedral : 14.012 126.565 4456 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.35 % Allowed : 16.71 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2440 helix: 0.53 (0.14), residues: 1484 sheet: -2.65 (0.56), residues: 64 loop : -0.94 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE A 415 TYR 0.011 0.002 TYR C 324 ARG 0.009 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 3.437 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: A 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 174 ASN cc_start: 0.7467 (t0) cc_final: 0.6957 (t0) REVERT: A 262 LYS cc_start: 0.8772 (tttm) cc_final: 0.7983 (ttpp) REVERT: A 303 GLU cc_start: 0.7691 (mp0) cc_final: 0.7286 (mp0) REVERT: A 314 LYS cc_start: 0.7256 (ttpt) cc_final: 0.6844 (ttmm) REVERT: A 322 LYS cc_start: 0.7733 (tmmt) cc_final: 0.7361 (mtpm) REVERT: A 492 ARG cc_start: 0.6255 (tpp80) cc_final: 0.5657 (tpp80) REVERT: A 596 GLN cc_start: 0.6759 (mt0) cc_final: 0.5948 (mm-40) REVERT: A 622 GLU cc_start: 0.7880 (pm20) cc_final: 0.7371 (pm20) REVERT: A 628 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7334 (mpp-170) REVERT: A 635 ASP cc_start: 0.7125 (t70) cc_final: 0.6658 (p0) REVERT: B 51 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 160 ILE cc_start: 0.8626 (pp) cc_final: 0.8356 (pp) REVERT: B 167 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7931 (tp) REVERT: B 174 ASN cc_start: 0.7623 (t0) cc_final: 0.7062 (t0) REVERT: B 262 LYS cc_start: 0.8776 (tttm) cc_final: 0.7963 (ttpp) REVERT: B 314 LYS cc_start: 0.7367 (ttpt) cc_final: 0.6965 (ttmm) REVERT: B 322 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7408 (mtpm) REVERT: B 596 GLN cc_start: 0.6830 (mt0) cc_final: 0.6029 (mm-40) REVERT: B 602 VAL cc_start: 0.7890 (t) cc_final: 0.7592 (m) REVERT: B 628 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7407 (mpp-170) REVERT: B 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6614 (p0) REVERT: C 51 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 160 ILE cc_start: 0.8568 (pp) cc_final: 0.8298 (pp) REVERT: C 167 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7885 (tp) REVERT: C 174 ASN cc_start: 0.7556 (t0) cc_final: 0.7064 (t0) REVERT: C 262 LYS cc_start: 0.8768 (tttm) cc_final: 0.7962 (ttpp) REVERT: C 314 LYS cc_start: 0.7270 (ttpt) cc_final: 0.6864 (ttmm) REVERT: C 322 LYS cc_start: 0.7748 (tmmt) cc_final: 0.7354 (mtpm) REVERT: C 596 GLN cc_start: 0.6788 (mt0) cc_final: 0.5996 (mm-40) REVERT: C 602 VAL cc_start: 0.7825 (t) cc_final: 0.7551 (m) REVERT: C 628 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7351 (mpp-170) REVERT: C 635 ASP cc_start: 0.7082 (t70) cc_final: 0.6619 (p0) REVERT: D 51 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7595 (tt) REVERT: D 113 GLU cc_start: 0.8284 (tt0) cc_final: 0.8059 (tt0) REVERT: D 167 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7899 (tp) REVERT: D 174 ASN cc_start: 0.7646 (t0) cc_final: 0.7161 (t0) REVERT: D 262 LYS cc_start: 0.8785 (tttm) cc_final: 0.7990 (ttpp) REVERT: D 301 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7906 (mtpm) REVERT: D 303 GLU cc_start: 0.7713 (mp0) cc_final: 0.7045 (mp0) REVERT: D 314 LYS cc_start: 0.7305 (ttpt) cc_final: 0.6899 (ttmm) REVERT: D 322 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7385 (mtpm) REVERT: D 596 GLN cc_start: 0.6654 (mt0) cc_final: 0.5931 (mm-40) REVERT: D 622 GLU cc_start: 0.7916 (pm20) cc_final: 0.7410 (pm20) REVERT: D 628 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7374 (mpp-170) REVERT: D 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6609 (p0) outliers start: 50 outliers final: 25 residues processed: 350 average time/residue: 2.2987 time to fit residues: 940.7505 Evaluate side-chains 350 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 357 ASN C 31 GLN C 357 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21556 Z= 0.243 Angle : 0.586 6.673 29140 Z= 0.291 Chirality : 0.039 0.192 3220 Planarity : 0.004 0.072 3532 Dihedral : 13.793 118.552 4456 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 2.07 % Allowed : 17.00 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2440 helix: 0.69 (0.14), residues: 1456 sheet: -2.67 (0.56), residues: 64 loop : -0.94 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE A 211 TYR 0.013 0.001 TYR A 216 ARG 0.009 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 329 time to evaluate : 3.087 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: A 51 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 174 ASN cc_start: 0.7451 (t0) cc_final: 0.6943 (t0) REVERT: A 262 LYS cc_start: 0.8766 (tttm) cc_final: 0.7975 (ttpp) REVERT: A 303 GLU cc_start: 0.7704 (mp0) cc_final: 0.7283 (mp0) REVERT: A 314 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6837 (ttmm) REVERT: A 322 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7347 (mtpm) REVERT: A 492 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (tpp80) REVERT: A 596 GLN cc_start: 0.6717 (mt0) cc_final: 0.5945 (mm-40) REVERT: A 622 GLU cc_start: 0.7880 (pm20) cc_final: 0.7367 (pm20) REVERT: A 628 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7328 (mpp-170) REVERT: A 635 ASP cc_start: 0.7170 (t70) cc_final: 0.6613 (p0) REVERT: B 51 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7591 (tt) REVERT: B 160 ILE cc_start: 0.8632 (pp) cc_final: 0.8355 (pp) REVERT: B 174 ASN cc_start: 0.7614 (t0) cc_final: 0.7068 (t0) REVERT: B 262 LYS cc_start: 0.8771 (tttm) cc_final: 0.7958 (ttpp) REVERT: B 314 LYS cc_start: 0.7358 (ttpt) cc_final: 0.6954 (ttmm) REVERT: B 322 LYS cc_start: 0.7801 (tmmt) cc_final: 0.7391 (mtpm) REVERT: B 596 GLN cc_start: 0.6784 (mt0) cc_final: 0.6010 (mm-40) REVERT: B 602 VAL cc_start: 0.7891 (t) cc_final: 0.7593 (m) REVERT: B 628 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7399 (mpp-170) REVERT: B 635 ASP cc_start: 0.7174 (t70) cc_final: 0.6641 (p0) REVERT: C 51 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7555 (tt) REVERT: C 160 ILE cc_start: 0.8575 (pp) cc_final: 0.8300 (pp) REVERT: C 174 ASN cc_start: 0.7541 (t0) cc_final: 0.6970 (t0) REVERT: C 262 LYS cc_start: 0.8763 (tttm) cc_final: 0.7913 (ttpp) REVERT: C 314 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6849 (ttmm) REVERT: C 322 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7338 (mtpm) REVERT: C 596 GLN cc_start: 0.6738 (mt0) cc_final: 0.5947 (mm-40) REVERT: C 602 VAL cc_start: 0.7819 (t) cc_final: 0.7544 (m) REVERT: C 628 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7336 (mpp-170) REVERT: C 635 ASP cc_start: 0.7155 (t70) cc_final: 0.6614 (p0) REVERT: D 51 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7590 (tt) REVERT: D 113 GLU cc_start: 0.8258 (tt0) cc_final: 0.8030 (tt0) REVERT: D 174 ASN cc_start: 0.7589 (t0) cc_final: 0.7126 (t0) REVERT: D 262 LYS cc_start: 0.8795 (tttm) cc_final: 0.8000 (ttpp) REVERT: D 303 GLU cc_start: 0.7700 (mp0) cc_final: 0.7086 (mp0) REVERT: D 314 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6880 (ttmm) REVERT: D 322 LYS cc_start: 0.7768 (tmmt) cc_final: 0.7363 (mtpm) REVERT: D 596 GLN cc_start: 0.6673 (mt0) cc_final: 0.5924 (mm-40) REVERT: D 622 GLU cc_start: 0.7907 (pm20) cc_final: 0.7393 (pm20) REVERT: D 628 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7373 (mpp-170) REVERT: D 635 ASP cc_start: 0.7149 (t70) cc_final: 0.6620 (p0) outliers start: 44 outliers final: 24 residues processed: 356 average time/residue: 2.2828 time to fit residues: 950.3716 Evaluate side-chains 348 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 320 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 243 optimal weight: 0.0170 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 357 ASN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21556 Z= 0.162 Angle : 0.564 6.605 29140 Z= 0.281 Chirality : 0.037 0.154 3220 Planarity : 0.004 0.051 3532 Dihedral : 12.878 107.672 4456 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 1.93 % Allowed : 17.47 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2440 helix: 0.88 (0.14), residues: 1460 sheet: -2.61 (0.56), residues: 64 loop : -0.77 (0.23), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 613 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE A 211 TYR 0.012 0.001 TYR B 324 ARG 0.010 0.000 ARG A 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 335 time to evaluate : 2.979 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: A 51 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7551 (tt) REVERT: A 174 ASN cc_start: 0.7341 (t0) cc_final: 0.7036 (t0) REVERT: A 262 LYS cc_start: 0.8775 (tttm) cc_final: 0.7983 (ttpp) REVERT: A 303 GLU cc_start: 0.7710 (mp0) cc_final: 0.7304 (mp0) REVERT: A 314 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6814 (ttmm) REVERT: A 322 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7312 (mtpm) REVERT: A 492 ARG cc_start: 0.6294 (tpp80) cc_final: 0.5659 (tpp80) REVERT: A 596 GLN cc_start: 0.6705 (mt0) cc_final: 0.5926 (mm-40) REVERT: A 622 GLU cc_start: 0.7859 (pm20) cc_final: 0.7358 (pm20) REVERT: A 628 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7305 (mpp-170) REVERT: A 635 ASP cc_start: 0.7121 (t70) cc_final: 0.6604 (p0) REVERT: B 51 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7597 (tt) REVERT: B 153 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7920 (mtt90) REVERT: B 160 ILE cc_start: 0.8605 (pp) cc_final: 0.8347 (pp) REVERT: B 174 ASN cc_start: 0.7579 (t0) cc_final: 0.7036 (t0) REVERT: B 262 LYS cc_start: 0.8756 (tttm) cc_final: 0.7952 (ttpp) REVERT: B 314 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6920 (ttmm) REVERT: B 322 LYS cc_start: 0.7806 (tmmt) cc_final: 0.7377 (mtpm) REVERT: B 596 GLN cc_start: 0.6774 (mt0) cc_final: 0.5989 (mm-40) REVERT: B 602 VAL cc_start: 0.7904 (t) cc_final: 0.7615 (m) REVERT: B 628 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7375 (mpp-170) REVERT: B 635 ASP cc_start: 0.7135 (t70) cc_final: 0.6673 (p0) REVERT: C 51 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7570 (tt) REVERT: C 160 ILE cc_start: 0.8557 (pp) cc_final: 0.8301 (pp) REVERT: C 174 ASN cc_start: 0.7464 (t0) cc_final: 0.6951 (t0) REVERT: C 262 LYS cc_start: 0.8751 (tttm) cc_final: 0.7954 (ttpp) REVERT: C 314 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6828 (ttmm) REVERT: C 322 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7310 (mtpm) REVERT: C 481 MET cc_start: 0.6875 (mtt) cc_final: 0.6659 (mtp) REVERT: C 596 GLN cc_start: 0.6722 (mt0) cc_final: 0.5912 (mm-40) REVERT: C 602 VAL cc_start: 0.7815 (t) cc_final: 0.7545 (m) REVERT: C 628 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7306 (mpp-170) REVERT: C 635 ASP cc_start: 0.7093 (t70) cc_final: 0.6596 (p0) REVERT: D 51 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7572 (tt) REVERT: D 113 GLU cc_start: 0.8244 (tt0) cc_final: 0.8031 (tt0) REVERT: D 160 ILE cc_start: 0.8600 (pp) cc_final: 0.8353 (pp) REVERT: D 174 ASN cc_start: 0.7606 (t0) cc_final: 0.7058 (t0) REVERT: D 262 LYS cc_start: 0.8779 (tttm) cc_final: 0.7993 (ttpp) REVERT: D 303 GLU cc_start: 0.7693 (mp0) cc_final: 0.7060 (mp0) REVERT: D 314 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6858 (ttmm) REVERT: D 322 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7341 (mtpm) REVERT: D 596 GLN cc_start: 0.6703 (mt0) cc_final: 0.5995 (mm-40) REVERT: D 628 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7339 (mpp-170) REVERT: D 635 ASP cc_start: 0.7121 (t70) cc_final: 0.6622 (p0) outliers start: 41 outliers final: 22 residues processed: 360 average time/residue: 2.3881 time to fit residues: 1006.8168 Evaluate side-chains 349 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 322 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 357 ASN C 357 ASN D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124272 restraints weight = 67016.955| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.14 r_work: 0.3417 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21556 Z= 0.205 Angle : 0.568 6.339 29140 Z= 0.283 Chirality : 0.038 0.184 3220 Planarity : 0.004 0.064 3532 Dihedral : 12.853 100.793 4456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.79 % Allowed : 17.75 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2440 helix: 0.92 (0.14), residues: 1460 sheet: -2.63 (0.55), residues: 64 loop : -0.76 (0.23), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 613 HIS 0.003 0.001 HIS B 201 PHE 0.010 0.001 PHE A 211 TYR 0.010 0.001 TYR B 324 ARG 0.010 0.000 ARG D 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16624.50 seconds wall clock time: 289 minutes 39.63 seconds (17379.63 seconds total)