Starting phenix.real_space_refine on Wed Feb 14 06:55:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyl_21968/02_2024/6wyl_21968.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5826 2.51 5 N 1395 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 257": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C GLU 416": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2940 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Chain: "B" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2940 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Chain: "C" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2940 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.58 Number of scatterers: 8847 At special positions: 0 Unit cell: (111.418, 104.516, 77.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1572 8.00 N 1395 7.00 C 5826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.543A pdb=" N HIS A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 73 removed outlier: 4.237A pdb=" N ALA A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.827A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.674A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 108 Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.846A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 150 through 171 removed outlier: 4.240A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.690A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 255 removed outlier: 3.694A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 275 removed outlier: 3.633A pdb=" N LYS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 4.411A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Proline residue: A 304 - end of helix removed outlier: 3.749A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.147A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.734A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 32 removed outlier: 3.544A pdb=" N HIS B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 73 removed outlier: 4.237A pdb=" N ALA B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 3.826A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.673A pdb=" N ILE B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 108 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.846A pdb=" N ILE B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 150 through 171 removed outlier: 4.205A pdb=" N THR B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 220 removed outlier: 3.690A pdb=" N TYR B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 223 through 255 removed outlier: 3.694A pdb=" N GLU B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 275 removed outlier: 3.633A pdb=" N LYS B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 removed outlier: 4.411A pdb=" N VAL B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 Proline residue: B 304 - end of helix removed outlier: 3.748A pdb=" N THR B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 352 Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.147A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 416 removed outlier: 3.733A pdb=" N ILE B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 32 removed outlier: 3.544A pdb=" N HIS C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 73 removed outlier: 4.238A pdb=" N ALA C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 3.826A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 3.674A pdb=" N ILE C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 108 Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.846A pdb=" N ILE C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 150 through 171 removed outlier: 4.213A pdb=" N THR C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 220 removed outlier: 3.690A pdb=" N TYR C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 223 through 255 removed outlier: 3.695A pdb=" N GLU C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.632A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 removed outlier: 4.411A pdb=" N VAL C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Proline residue: C 304 - end of helix removed outlier: 3.748A pdb=" N THR C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 330 Processing helix chain 'C' and resid 334 through 352 Processing helix chain 'C' and resid 357 through 371 removed outlier: 4.147A pdb=" N ILE C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 416 removed outlier: 3.734A pdb=" N ILE C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2322 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: 2.55 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2721 1.34 - 1.46: 1545 1.46 - 1.57: 4623 1.57 - 1.69: 0 1.69 - 1.80: 102 Bond restraints: 8991 Sorted by residual: bond pdb=" N ASN C 148 " pdb=" CA ASN C 148 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.44e+00 bond pdb=" N ASN B 148 " pdb=" CA ASN B 148 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.22e-02 6.72e+03 7.84e+00 bond pdb=" CB ILE B 187 " pdb=" CG2 ILE B 187 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.51e+00 bond pdb=" CB ILE A 187 " pdb=" CG2 ILE A 187 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.38e+00 bond pdb=" CB ILE C 187 " pdb=" CG2 ILE C 187 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.32e+00 ... (remaining 8986 not shown) Histogram of bond angle deviations from ideal: 96.20 - 103.22: 126 103.22 - 110.25: 2265 110.25 - 117.28: 4499 117.28 - 124.30: 5266 124.30 - 131.33: 78 Bond angle restraints: 12234 Sorted by residual: angle pdb=" C GLN A 150 " pdb=" N VAL A 151 " pdb=" CA VAL A 151 " ideal model delta sigma weight residual 120.72 127.63 -6.91 1.22e+00 6.72e-01 3.21e+01 angle pdb=" C GLN C 150 " pdb=" N VAL C 151 " pdb=" CA VAL C 151 " ideal model delta sigma weight residual 120.72 127.52 -6.80 1.22e+00 6.72e-01 3.11e+01 angle pdb=" C GLN B 150 " pdb=" N VAL B 151 " pdb=" CA VAL B 151 " ideal model delta sigma weight residual 120.72 127.50 -6.78 1.22e+00 6.72e-01 3.09e+01 angle pdb=" N GLN A 150 " pdb=" CA GLN A 150 " pdb=" CB GLN A 150 " ideal model delta sigma weight residual 110.60 104.63 5.97 1.52e+00 4.33e-01 1.54e+01 angle pdb=" N GLN B 150 " pdb=" CA GLN B 150 " pdb=" CB GLN B 150 " ideal model delta sigma weight residual 110.60 104.73 5.87 1.52e+00 4.33e-01 1.49e+01 ... (remaining 12229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 4677 11.92 - 23.85: 491 23.85 - 35.77: 127 35.77 - 47.70: 39 47.70 - 59.62: 9 Dihedral angle restraints: 5343 sinusoidal: 1947 harmonic: 3396 Sorted by residual: dihedral pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" N VAL B 222 " pdb=" CA VAL B 222 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N VAL A 222 " pdb=" CA VAL A 222 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY C 221 " pdb=" C GLY C 221 " pdb=" N VAL C 222 " pdb=" CA VAL C 222 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 910 0.038 - 0.076: 434 0.076 - 0.113: 170 0.113 - 0.151: 37 0.151 - 0.189: 9 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CB ILE C 160 " pdb=" CA ILE C 160 " pdb=" CG1 ILE C 160 " pdb=" CG2 ILE C 160 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB ILE A 160 " pdb=" CA ILE A 160 " pdb=" CG1 ILE A 160 " pdb=" CG2 ILE A 160 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CB ILE B 160 " pdb=" CA ILE B 160 " pdb=" CG1 ILE B 160 " pdb=" CG2 ILE B 160 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1557 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 59 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 60 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 59 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 60 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 59 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.80e+00 pdb=" N PRO C 60 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.031 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2002 2.77 - 3.30: 9862 3.30 - 3.83: 14305 3.83 - 4.37: 15888 4.37 - 4.90: 27150 Nonbonded interactions: 69207 Sorted by model distance: nonbonded pdb=" N SER B 278 " pdb=" OXT ASP B 501 " model vdw 2.237 2.520 nonbonded pdb=" N SER A 278 " pdb=" OXT ASP A 501 " model vdw 2.237 2.520 nonbonded pdb=" N SER C 278 " pdb=" OXT ASP C 501 " model vdw 2.238 2.520 nonbonded pdb=" O VAL C 355 " pdb=" N ASP C 501 " model vdw 2.290 2.520 nonbonded pdb=" O VAL A 355 " pdb=" N ASP A 501 " model vdw 2.290 2.520 ... (remaining 69202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.210 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.650 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.012 0.090 8991 Z= 0.788 Angle : 0.912 7.016 12234 Z= 0.533 Chirality : 0.050 0.189 1560 Planarity : 0.006 0.055 1488 Dihedral : 11.334 59.622 3183 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -1.66 (0.21), residues: 1179 helix: -0.76 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : -2.15 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 32 PHE 0.012 0.002 PHE B 63 TYR 0.035 0.003 TYR B 299 ARG 0.007 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6862 (mmp-170) cc_final: 0.6609 (ttt180) REVERT: A 244 LEU cc_start: 0.8950 (mt) cc_final: 0.8657 (mm) REVERT: A 270 LEU cc_start: 0.8492 (mm) cc_final: 0.8226 (mt) REVERT: A 311 MET cc_start: 0.8812 (mtm) cc_final: 0.8497 (mtp) REVERT: A 385 MET cc_start: 0.8742 (mtt) cc_final: 0.8522 (mtp) REVERT: B 85 ILE cc_start: 0.8482 (mm) cc_final: 0.8163 (tp) REVERT: B 194 MET cc_start: 0.8766 (mmm) cc_final: 0.8210 (mmt) REVERT: B 267 ASP cc_start: 0.8136 (t0) cc_final: 0.7792 (t0) REVERT: B 311 MET cc_start: 0.8671 (mtm) cc_final: 0.8229 (mtp) REVERT: B 385 MET cc_start: 0.8626 (mtt) cc_final: 0.8292 (mtp) REVERT: C 77 ARG cc_start: 0.6939 (mmp-170) cc_final: 0.6533 (ttt180) REVERT: C 405 ASP cc_start: 0.8073 (m-30) cc_final: 0.7815 (m-30) REVERT: B 501 ASP cc_start: 0.7982 (m-30) cc_final: 0.7564 (m-30) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1752 time to fit residues: 82.3831 Evaluate side-chains 231 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8991 Z= 0.223 Angle : 0.679 11.417 12234 Z= 0.359 Chirality : 0.043 0.297 1560 Planarity : 0.005 0.043 1488 Dihedral : 5.831 76.989 1263 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.62 % Allowed : 11.08 % Favored : 85.30 % 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: 1.27 (0.24), residues: 1179 helix: 1.21 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.023 0.002 PHE C 248 TYR 0.023 0.002 TYR C 299 ARG 0.003 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 285 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6354 (mmp-170) cc_final: 0.5905 (ttt180) REVERT: A 85 ILE cc_start: 0.8536 (mm) cc_final: 0.8249 (tp) REVERT: A 242 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: A 248 PHE cc_start: 0.7916 (m-80) cc_final: 0.7467 (m-80) REVERT: A 369 SER cc_start: 0.9464 (t) cc_final: 0.9171 (p) REVERT: A 395 MET cc_start: 0.6327 (mtm) cc_final: 0.6100 (mtm) REVERT: A 405 ASP cc_start: 0.8096 (m-30) cc_final: 0.7853 (m-30) REVERT: B 85 ILE cc_start: 0.8523 (mm) cc_final: 0.8225 (tp) REVERT: B 88 TYR cc_start: 0.8625 (t80) cc_final: 0.7842 (t80) REVERT: B 181 GLU cc_start: 0.7503 (tp30) cc_final: 0.7244 (tp30) REVERT: B 244 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 267 ASP cc_start: 0.7868 (t0) cc_final: 0.7659 (t0) REVERT: B 270 LEU cc_start: 0.8387 (mm) cc_final: 0.8170 (mt) REVERT: B 287 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8316 (ttp-170) REVERT: B 368 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 395 MET cc_start: 0.5969 (mtm) cc_final: 0.5580 (mtm) REVERT: B 406 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 40 LYS cc_start: 0.8701 (tttm) cc_final: 0.8415 (ttmt) REVERT: C 77 ARG cc_start: 0.6268 (mmp-170) cc_final: 0.5843 (ttp-170) REVERT: C 89 TYR cc_start: 0.8689 (m-10) cc_final: 0.8220 (m-10) REVERT: C 131 VAL cc_start: 0.8585 (p) cc_final: 0.8368 (t) REVERT: C 185 ASP cc_start: 0.7414 (m-30) cc_final: 0.7206 (m-30) REVERT: C 210 PHE cc_start: 0.8523 (t80) cc_final: 0.8319 (t80) REVERT: C 244 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 369 SER cc_start: 0.9446 (t) cc_final: 0.9161 (p) REVERT: C 385 MET cc_start: 0.8863 (mtm) cc_final: 0.8518 (mtp) REVERT: C 399 MET cc_start: 0.8700 (tmm) cc_final: 0.7754 (tmm) REVERT: C 405 ASP cc_start: 0.8154 (m-30) cc_final: 0.7907 (m-30) outliers start: 34 outliers final: 23 residues processed: 299 average time/residue: 0.1764 time to fit residues: 75.3133 Evaluate side-chains 254 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 366 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.0670 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8991 Z= 0.196 Angle : 0.652 11.316 12234 Z= 0.333 Chirality : 0.044 0.316 1560 Planarity : 0.004 0.037 1488 Dihedral : 5.600 77.614 1263 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.47 % Allowed : 16.19 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1179 helix: 1.70 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.04 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.019 0.001 PHE B 261 TYR 0.021 0.001 TYR B 299 ARG 0.003 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.030 Fit side-chains REVERT: A 77 ARG cc_start: 0.6211 (mmp-170) cc_final: 0.5844 (ttp-170) REVERT: A 85 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 242 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: A 247 TYR cc_start: 0.8262 (m-80) cc_final: 0.7719 (m-80) REVERT: A 311 MET cc_start: 0.8702 (mtm) cc_final: 0.8430 (mtp) REVERT: A 369 SER cc_start: 0.9507 (t) cc_final: 0.9265 (p) REVERT: B 88 TYR cc_start: 0.8653 (t80) cc_final: 0.7814 (t80) REVERT: B 267 ASP cc_start: 0.7789 (t0) cc_final: 0.7568 (t0) REVERT: B 287 ARG cc_start: 0.8639 (ttp-170) cc_final: 0.8273 (ttp-170) REVERT: B 406 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 99 LEU cc_start: 0.8268 (tt) cc_final: 0.8060 (mt) REVERT: C 248 PHE cc_start: 0.7715 (m-80) cc_final: 0.7296 (m-80) REVERT: C 362 MET cc_start: 0.7295 (mmt) cc_final: 0.7003 (mmt) REVERT: C 385 MET cc_start: 0.8638 (mtm) cc_final: 0.8237 (mtp) REVERT: C 399 MET cc_start: 0.8366 (tmm) cc_final: 0.8012 (tmm) outliers start: 42 outliers final: 25 residues processed: 261 average time/residue: 0.1576 time to fit residues: 60.9368 Evaluate side-chains 243 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain A residue 501 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8991 Z= 0.228 Angle : 0.676 13.846 12234 Z= 0.334 Chirality : 0.043 0.207 1560 Planarity : 0.004 0.037 1488 Dihedral : 5.610 79.567 1263 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.32 % Allowed : 17.25 % Favored : 77.42 % 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: 2.10 (0.25), residues: 1179 helix: 1.75 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -1.03 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 332 PHE 0.021 0.001 PHE B 261 TYR 0.028 0.001 TYR A 88 ARG 0.011 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 1.050 Fit side-chains REVERT: A 77 ARG cc_start: 0.6193 (mmp-170) cc_final: 0.5800 (ttp-170) REVERT: A 89 TYR cc_start: 0.8781 (m-10) cc_final: 0.8185 (m-10) REVERT: A 242 GLN cc_start: 0.8751 (tt0) cc_final: 0.8454 (tm-30) REVERT: A 247 TYR cc_start: 0.8293 (m-80) cc_final: 0.7655 (m-80) REVERT: A 369 SER cc_start: 0.9511 (t) cc_final: 0.9261 (p) REVERT: A 397 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7607 (mpp80) REVERT: B 85 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8280 (tp) REVERT: B 88 TYR cc_start: 0.8675 (t80) cc_final: 0.7902 (t80) REVERT: B 406 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8524 (mm) REVERT: C 248 PHE cc_start: 0.7790 (m-80) cc_final: 0.7436 (m-80) outliers start: 50 outliers final: 37 residues processed: 247 average time/residue: 0.1604 time to fit residues: 58.4241 Evaluate side-chains 259 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain C residue 501 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8991 Z= 0.252 Angle : 0.678 14.708 12234 Z= 0.334 Chirality : 0.043 0.199 1560 Planarity : 0.004 0.038 1488 Dihedral : 5.652 80.578 1263 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.07 % Allowed : 17.25 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.25), residues: 1179 helix: 1.73 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -0.95 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 32 PHE 0.022 0.001 PHE A 324 TYR 0.020 0.001 TYR C 88 ARG 0.009 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 0.945 Fit side-chains REVERT: A 77 ARG cc_start: 0.6203 (mmp-170) cc_final: 0.5731 (ttp-170) REVERT: A 169 MET cc_start: 0.8296 (tpp) cc_final: 0.7955 (mtt) REVERT: A 242 GLN cc_start: 0.8795 (tt0) cc_final: 0.8492 (tm-30) REVERT: A 247 TYR cc_start: 0.8269 (m-80) cc_final: 0.7592 (m-80) REVERT: A 369 SER cc_start: 0.9525 (t) cc_final: 0.9269 (p) REVERT: B 85 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 88 TYR cc_start: 0.8616 (t80) cc_final: 0.7962 (t80) REVERT: B 369 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9322 (p) REVERT: C 99 LEU cc_start: 0.8313 (tt) cc_final: 0.7989 (mt) REVERT: C 248 PHE cc_start: 0.7919 (m-80) cc_final: 0.7590 (m-80) outliers start: 57 outliers final: 44 residues processed: 251 average time/residue: 0.1623 time to fit residues: 59.4350 Evaluate side-chains 267 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain C residue 501 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 8991 Z= 0.452 Angle : 0.805 15.186 12234 Z= 0.406 Chirality : 0.046 0.347 1560 Planarity : 0.005 0.040 1488 Dihedral : 6.120 87.115 1263 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.60 % Allowed : 18.21 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1179 helix: 1.40 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 32 PHE 0.026 0.002 PHE B 261 TYR 0.017 0.002 TYR C 88 ARG 0.004 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 208 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6306 (mmp-170) cc_final: 0.5723 (ttp-170) REVERT: A 169 MET cc_start: 0.8388 (tpp) cc_final: 0.8055 (mtt) REVERT: A 247 TYR cc_start: 0.8639 (m-80) cc_final: 0.8390 (m-80) REVERT: B 85 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 88 TYR cc_start: 0.8642 (t80) cc_final: 0.8035 (t80) REVERT: B 312 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8840 (p0) REVERT: B 369 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9279 (p) REVERT: C 77 ARG cc_start: 0.6387 (mmp-170) cc_final: 0.5745 (ttp-170) REVERT: C 281 THR cc_start: 0.8566 (p) cc_final: 0.8363 (p) REVERT: C 312 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8869 (p0) REVERT: C 362 MET cc_start: 0.7888 (mmt) cc_final: 0.7611 (mmt) REVERT: C 372 LEU cc_start: 0.7543 (mp) cc_final: 0.7107 (tt) REVERT: C 399 MET cc_start: 0.8752 (tmm) cc_final: 0.8325 (tmm) outliers start: 62 outliers final: 45 residues processed: 235 average time/residue: 0.1606 time to fit residues: 55.5914 Evaluate side-chains 252 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 501 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8991 Z= 0.209 Angle : 0.672 15.924 12234 Z= 0.332 Chirality : 0.043 0.191 1560 Planarity : 0.004 0.038 1488 Dihedral : 5.829 83.379 1263 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.26 % Allowed : 21.09 % Favored : 74.65 % 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: 2.06 (0.24), residues: 1179 helix: 1.73 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.87 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 32 PHE 0.021 0.001 PHE B 324 TYR 0.020 0.001 TYR A 88 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 1.034 Fit side-chains REVERT: A 77 ARG cc_start: 0.6087 (mmp-170) cc_final: 0.5676 (ttp-170) REVERT: A 242 GLN cc_start: 0.8699 (tt0) cc_final: 0.8457 (tm-30) REVERT: A 247 TYR cc_start: 0.8404 (m-80) cc_final: 0.7680 (m-80) REVERT: B 11 PRO cc_start: 0.8214 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: B 85 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 88 TYR cc_start: 0.8589 (t80) cc_final: 0.7963 (t80) REVERT: B 312 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8692 (p0) REVERT: C 11 PRO cc_start: 0.7937 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: C 42 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: C 77 ARG cc_start: 0.6195 (mmp-170) cc_final: 0.5685 (ttp-170) REVERT: C 99 LEU cc_start: 0.8357 (tt) cc_final: 0.8059 (mp) REVERT: C 247 TYR cc_start: 0.8226 (m-10) cc_final: 0.7900 (m-80) REVERT: C 287 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8445 (ttp-170) REVERT: C 362 MET cc_start: 0.7621 (mmt) cc_final: 0.7342 (mmt) outliers start: 40 outliers final: 30 residues processed: 249 average time/residue: 0.1587 time to fit residues: 58.5121 Evaluate side-chains 254 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 8991 Z= 0.223 Angle : 0.705 16.547 12234 Z= 0.343 Chirality : 0.044 0.276 1560 Planarity : 0.004 0.037 1488 Dihedral : 5.641 80.696 1263 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.37 % Allowed : 21.51 % Favored : 74.12 % 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: 2.13 (0.25), residues: 1179 helix: 1.72 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.50 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.023 0.001 PHE B 261 TYR 0.016 0.001 TYR B 299 ARG 0.004 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 1.016 Fit side-chains REVERT: A 42 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: A 77 ARG cc_start: 0.6068 (mmp-170) cc_final: 0.5629 (ttp-170) REVERT: A 169 MET cc_start: 0.8285 (tpp) cc_final: 0.7874 (mtt) REVERT: A 194 MET cc_start: 0.8854 (mmm) cc_final: 0.8641 (mmt) REVERT: A 242 GLN cc_start: 0.8672 (tt0) cc_final: 0.8405 (tm-30) REVERT: A 247 TYR cc_start: 0.8363 (m-80) cc_final: 0.7671 (m-80) REVERT: A 369 SER cc_start: 0.9492 (t) cc_final: 0.9275 (p) REVERT: B 85 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 88 TYR cc_start: 0.8559 (t80) cc_final: 0.7991 (t80) REVERT: B 108 ASN cc_start: 0.6041 (p0) cc_final: 0.5789 (p0) REVERT: B 312 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8684 (p0) REVERT: C 11 PRO cc_start: 0.7899 (Cg_exo) cc_final: 0.7507 (Cg_endo) REVERT: C 42 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: C 77 ARG cc_start: 0.6205 (mmp-170) cc_final: 0.5678 (ttp-170) REVERT: C 99 LEU cc_start: 0.8327 (tt) cc_final: 0.8027 (mp) REVERT: C 247 TYR cc_start: 0.8164 (m-10) cc_final: 0.7903 (m-80) REVERT: C 287 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8352 (ttp-170) REVERT: C 362 MET cc_start: 0.7703 (mmt) cc_final: 0.7415 (mmt) REVERT: C 397 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6749 (mtp85) outliers start: 41 outliers final: 33 residues processed: 242 average time/residue: 0.1722 time to fit residues: 61.0313 Evaluate side-chains 255 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8991 Z= 0.191 Angle : 0.685 16.543 12234 Z= 0.333 Chirality : 0.044 0.243 1560 Planarity : 0.004 0.037 1488 Dihedral : 5.358 76.899 1263 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.94 % Allowed : 22.36 % Favored : 73.70 % 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: 2.26 (0.25), residues: 1179 helix: 1.82 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.49 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 332 PHE 0.024 0.001 PHE B 261 TYR 0.028 0.001 TYR A 88 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 0.964 Fit side-chains REVERT: A 42 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: A 77 ARG cc_start: 0.6018 (mmp-170) cc_final: 0.5600 (ttp-170) REVERT: A 169 MET cc_start: 0.8218 (tpp) cc_final: 0.7796 (mtt) REVERT: A 242 GLN cc_start: 0.8633 (tt0) cc_final: 0.8426 (tm-30) REVERT: A 247 TYR cc_start: 0.8200 (m-80) cc_final: 0.7619 (m-80) REVERT: A 325 ILE cc_start: 0.8903 (mm) cc_final: 0.8606 (mt) REVERT: A 369 SER cc_start: 0.9515 (t) cc_final: 0.9296 (p) REVERT: B 11 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7857 (Cg_endo) REVERT: B 85 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 88 TYR cc_start: 0.8550 (t80) cc_final: 0.7926 (t80) REVERT: B 108 ASN cc_start: 0.6190 (p0) cc_final: 0.5977 (p0) REVERT: B 267 ASP cc_start: 0.8066 (t0) cc_final: 0.7732 (t0) REVERT: B 312 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8525 (p0) REVERT: B 403 THR cc_start: 0.9109 (m) cc_final: 0.8690 (p) REVERT: C 11 PRO cc_start: 0.7903 (Cg_exo) cc_final: 0.7544 (Cg_endo) REVERT: C 99 LEU cc_start: 0.8361 (tt) cc_final: 0.8084 (mp) REVERT: C 247 TYR cc_start: 0.8028 (m-10) cc_final: 0.7804 (m-80) REVERT: C 287 ARG cc_start: 0.8649 (ttp-170) cc_final: 0.8414 (ttp-170) REVERT: C 362 MET cc_start: 0.7580 (mmt) cc_final: 0.7160 (mmt) REVERT: C 397 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7635 (mtm180) REVERT: C 399 MET cc_start: 0.8481 (tmm) cc_final: 0.8233 (tmm) outliers start: 37 outliers final: 30 residues processed: 244 average time/residue: 0.1578 time to fit residues: 57.1207 Evaluate side-chains 250 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 8991 Z= 0.217 Angle : 0.717 16.996 12234 Z= 0.345 Chirality : 0.044 0.290 1560 Planarity : 0.004 0.037 1488 Dihedral : 5.211 74.501 1263 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.83 % Allowed : 23.86 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1179 helix: 1.76 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 332 PHE 0.023 0.001 PHE B 261 TYR 0.015 0.001 TYR B 299 ARG 0.004 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 0.949 Fit side-chains REVERT: A 42 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 77 ARG cc_start: 0.6029 (mmp-170) cc_final: 0.5597 (ttp-170) REVERT: A 169 MET cc_start: 0.8217 (tpp) cc_final: 0.7811 (mtt) REVERT: A 242 GLN cc_start: 0.8634 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 247 TYR cc_start: 0.8191 (m-80) cc_final: 0.7618 (m-80) REVERT: B 11 PRO cc_start: 0.8071 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: B 85 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 88 TYR cc_start: 0.8531 (t80) cc_final: 0.8066 (t80) REVERT: B 108 ASN cc_start: 0.6202 (p0) cc_final: 0.5961 (p0) REVERT: B 287 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8261 (tmm160) REVERT: B 312 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8467 (p0) REVERT: B 403 THR cc_start: 0.9090 (m) cc_final: 0.8669 (p) REVERT: C 11 PRO cc_start: 0.7916 (Cg_exo) cc_final: 0.7555 (Cg_endo) REVERT: C 99 LEU cc_start: 0.8401 (tt) cc_final: 0.8102 (mp) REVERT: C 287 ARG cc_start: 0.8640 (ttp-170) cc_final: 0.8410 (ttp-170) REVERT: C 372 LEU cc_start: 0.7384 (mp) cc_final: 0.7084 (tt) REVERT: C 397 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7694 (mtm180) REVERT: C 399 MET cc_start: 0.8455 (tmm) cc_final: 0.8240 (tmm) outliers start: 36 outliers final: 29 residues processed: 238 average time/residue: 0.1532 time to fit residues: 54.1573 Evaluate side-chains 245 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109960 restraints weight = 14385.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110238 restraints weight = 12543.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111121 restraints weight = 12372.677| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8991 Z= 0.214 Angle : 0.702 16.800 12234 Z= 0.340 Chirality : 0.044 0.271 1560 Planarity : 0.004 0.040 1488 Dihedral : 5.059 71.990 1263 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.83 % Allowed : 24.07 % Favored : 72.10 % 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: 2.29 (0.25), residues: 1179 helix: 1.82 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.023 0.001 PHE B 261 TYR 0.027 0.001 TYR A 88 ARG 0.004 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.75 seconds wall clock time: 34 minutes 48.62 seconds (2088.62 seconds total)