Starting phenix.real_space_refine on Mon Mar 18 09:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/03_2024/7mpg_23933.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 12828 2.51 5 N 3390 2.21 5 O 4040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1635 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.76, per 1000 atoms: 0.53 Number of scatterers: 20366 At special positions: 0 Unit cell: (196.88, 202.23, 128.4, 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 108 16.00 O 4040 8.00 N 3390 7.00 C 12828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.05 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.05 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.05 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 500 " Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 3.8 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 48 sheets defined 21.1% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.516A pdb=" N LYS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.790A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.800A pdb=" N VAL A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 369 through 372 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'B' and resid 73 through 96 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.649A pdb=" N LYS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.867A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 282' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 369 through 372 Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.568A pdb=" N LYS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.884A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 369 through 372 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.500A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 128 Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.788A pdb=" N LYS G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.582A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.733A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.692A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.536A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.900A pdb=" N LYS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 312 removed outlier: 6.077A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 311 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.231A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 244 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.563A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.625A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 308 through 312 removed outlier: 6.095A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR B 311 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.259A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 56 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 190 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 244 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.584A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.611A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AB5, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.146A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR C 311 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.151A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 190 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 244 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.657A pdb=" N ASN C 426 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 94 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG F 96 " --> pdb=" O MET F 100F" (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET F 100F" --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU G 105 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.174A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 144 through 149 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.305A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.387A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.231A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 33 " --> pdb=" O HIS I 49 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 115 through 118 removed outlier: 6.054A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 144 through 149 Processing sheet with id=AE3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.076A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AE8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 115 through 118 removed outlier: 5.921A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 144 through 149 950 hydrogen bonds defined for protein. 2403 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: 7.71 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6565 1.35 - 1.48: 5041 1.48 - 1.61: 8994 1.61 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 20744 Sorted by residual: bond pdb=" CA MET D 82 " pdb=" CB MET D 82 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP G 1 " pdb=" CA ASP G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP I 1 " pdb=" CA ASP I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 20739 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.97: 417 105.97 - 112.99: 11566 112.99 - 120.00: 6629 120.00 - 127.02: 9354 127.02 - 134.04: 191 Bond angle restraints: 28157 Sorted by residual: angle pdb=" CG1 VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.80 121.97 -11.17 2.20e+00 2.07e-01 2.58e+01 angle pdb=" CA CYS B 313 " pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " ideal model delta sigma weight residual 114.40 123.45 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C LYS B 272 " pdb=" N LEU B 273 " pdb=" CA LEU B 273 " ideal model delta sigma weight residual 120.54 125.77 -5.23 1.35e+00 5.49e-01 1.50e+01 angle pdb=" CA CYS C 313 " pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.43e+01 ... (remaining 28152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 12100 25.17 - 50.34: 519 50.34 - 75.52: 39 75.52 - 100.69: 18 100.69 - 125.86: 1 Dihedral angle restraints: 12677 sinusoidal: 4985 harmonic: 7692 Sorted by residual: dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.46 -57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS G 134 " pdb=" SG CYS G 134 " pdb=" SG CYS G 194 " pdb=" CB CYS G 194 " ideal model delta sinusoidal sigma weight residual 93.00 43.30 49.70 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CB CYS I 134 " pdb=" SG CYS I 134 " pdb=" SG CYS I 194 " pdb=" CB CYS I 194 " ideal model delta sinusoidal sigma weight residual 93.00 44.72 48.28 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 12674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 3284 0.333 - 0.667: 0 0.667 - 1.000: 0 1.000 - 1.334: 0 1.334 - 1.667: 2 Chirality restraints: 3286 Sorted by residual: chirality pdb=" CG LEU I 94 " pdb=" CB LEU I 94 " pdb=" CD1 LEU I 94 " pdb=" CD2 LEU I 94 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.95e+01 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.28e+01 chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3283 not shown) Planarity restraints: 3580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.76e+00 pdb=" CG TRP H 36 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 122 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO H 123 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 123 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 43 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 44 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 44 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 44 " -0.024 5.00e-02 4.00e+02 ... (remaining 3577 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 192 2.51 - 3.10: 16050 3.10 - 3.70: 30894 3.70 - 4.30: 43610 4.30 - 4.90: 72914 Nonbonded interactions: 163660 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 1.908 2.440 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 1.917 2.440 nonbonded pdb=" OG1 THR C 267 " pdb=" OD1 ASP C 269 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR B 267 " pdb=" OD1 ASP B 269 " model vdw 1.943 2.440 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 1.964 2.440 ... (remaining 163655 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' } ncs_group { reference = (chain 'D' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = (chain 'F' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.270 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 54.800 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.003 0.057 20744 Z= 0.218 Angle : 0.713 11.174 28157 Z= 0.414 Chirality : 0.058 1.667 3286 Planarity : 0.004 0.051 3579 Dihedral : 13.663 125.861 7619 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.25 (0.17), residues: 2610 helix: 0.18 (0.26), residues: 417 sheet: -0.62 (0.18), residues: 907 loop : -1.27 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 36 HIS 0.005 0.001 HIS G 37 PHE 0.016 0.001 PHE F 29 TYR 0.017 0.002 TYR D 100C ARG 0.006 0.001 ARG I 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8192 (tt) cc_final: 0.7991 (tt) REVERT: C 392 ASP cc_start: 0.7107 (t0) cc_final: 0.6877 (t0) REVERT: F 143 LYS cc_start: 0.6479 (mmtm) cc_final: 0.6174 (tmtt) REVERT: E 94 LEU cc_start: 0.6626 (mt) cc_final: 0.6183 (mt) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.3277 time to fit residues: 343.2573 Evaluate side-chains 405 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 109 optimal weight: 0.1980 chunk 67 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 81 GLN A 302 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 302 GLN B 460 ASN C 277 ASN C 284 GLN C 302 GLN F 76 ASN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 76 ASN I 3 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN D 76 ASN E 124 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20744 Z= 0.336 Angle : 0.750 11.401 28157 Z= 0.386 Chirality : 0.049 0.379 3286 Planarity : 0.005 0.056 3579 Dihedral : 6.494 104.446 2874 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 3.53 % Allowed : 11.50 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2610 helix: 0.92 (0.25), residues: 411 sheet: -0.57 (0.17), residues: 913 loop : -1.06 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 35 HIS 0.009 0.001 HIS E 37 PHE 0.030 0.002 PHE B 483 TYR 0.033 0.002 TYR D 100C ARG 0.014 0.001 ARG F 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 424 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7229 (tttm) REVERT: A 448 ASP cc_start: 0.6155 (t0) cc_final: 0.5864 (t0) REVERT: B 248 SER cc_start: 0.8108 (p) cc_final: 0.7612 (p) REVERT: C 448 ASP cc_start: 0.6314 (t0) cc_final: 0.6077 (t0) REVERT: F 34 MET cc_start: 0.7909 (mmt) cc_final: 0.7620 (mmt) REVERT: F 58 TYR cc_start: 0.7538 (m-10) cc_final: 0.7302 (m-10) REVERT: H 100 ASP cc_start: 0.7597 (t0) cc_final: 0.6522 (t0) REVERT: H 100 TYR cc_start: 0.7701 (m-80) cc_final: 0.7438 (m-80) REVERT: D 47 TRP cc_start: 0.8342 (t60) cc_final: 0.8037 (t60) REVERT: D 89 LEU cc_start: 0.7751 (tp) cc_final: 0.7453 (tp) outliers start: 83 outliers final: 38 residues processed: 475 average time/residue: 0.3058 time to fit residues: 223.8256 Evaluate side-chains 373 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 237 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 227 ASN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN F 76 ASN H 56 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 20744 Z= 0.397 Angle : 0.738 12.708 28157 Z= 0.380 Chirality : 0.048 0.352 3286 Planarity : 0.005 0.052 3579 Dihedral : 6.326 89.592 2874 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 5.11 % Allowed : 14.74 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2610 helix: 0.83 (0.26), residues: 429 sheet: -0.61 (0.17), residues: 904 loop : -1.15 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 35 HIS 0.007 0.002 HIS D 200 PHE 0.025 0.002 PHE D 67 TYR 0.035 0.002 TYR F 100D ARG 0.009 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 365 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9075 (m) REVERT: A 61 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 156 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7652 (tttm) REVERT: A 448 ASP cc_start: 0.6784 (t0) cc_final: 0.6502 (t0) REVERT: A 505 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6675 (t80) REVERT: B 49 ARG cc_start: 0.7746 (ttp80) cc_final: 0.6955 (ttp80) REVERT: C 141 LEU cc_start: 0.7691 (pp) cc_final: 0.7458 (pp) REVERT: C 448 ASP cc_start: 0.6402 (t0) cc_final: 0.5990 (t0) REVERT: C 460 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8334 (m-40) REVERT: H 47 TRP cc_start: 0.8021 (t60) cc_final: 0.7809 (t60) REVERT: H 58 TYR cc_start: 0.7864 (m-80) cc_final: 0.7592 (m-80) REVERT: H 100 ASP cc_start: 0.7807 (t0) cc_final: 0.7389 (t0) REVERT: H 100 TYR cc_start: 0.8033 (m-10) cc_final: 0.7244 (m-80) REVERT: H 100 TYR cc_start: 0.7696 (m-80) cc_final: 0.7458 (m-80) REVERT: H 100 TYR cc_start: 0.7883 (m-80) cc_final: 0.7097 (m-80) REVERT: D 58 TYR cc_start: 0.8001 (m-80) cc_final: 0.7637 (m-80) outliers start: 120 outliers final: 68 residues processed: 450 average time/residue: 0.2986 time to fit residues: 211.0991 Evaluate side-chains 389 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 316 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN D 76 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20744 Z= 0.186 Angle : 0.656 11.052 28157 Z= 0.332 Chirality : 0.046 0.378 3286 Planarity : 0.005 0.052 3579 Dihedral : 5.871 82.888 2874 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 3.45 % Allowed : 18.95 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2610 helix: 0.93 (0.26), residues: 438 sheet: -0.46 (0.17), residues: 900 loop : -1.01 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 47 HIS 0.005 0.001 HIS E 37 PHE 0.024 0.002 PHE A 483 TYR 0.021 0.001 TYR F 52A ARG 0.006 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 394 time to evaluate : 2.560 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7861 (ttp80) cc_final: 0.6931 (ttp80) REVERT: A 156 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7414 (tttm) REVERT: A 448 ASP cc_start: 0.6846 (t0) cc_final: 0.6474 (t0) REVERT: B 141 LEU cc_start: 0.7535 (pp) cc_final: 0.7252 (pp) REVERT: C 448 ASP cc_start: 0.6457 (t0) cc_final: 0.5995 (t0) REVERT: H 43 LYS cc_start: 0.7626 (mmmm) cc_final: 0.7415 (mmtp) REVERT: H 58 TYR cc_start: 0.7730 (m-80) cc_final: 0.7463 (m-80) REVERT: H 100 ASP cc_start: 0.7735 (t0) cc_final: 0.7082 (t0) REVERT: H 100 TYR cc_start: 0.7895 (m-10) cc_final: 0.7128 (m-80) REVERT: H 100 TYR cc_start: 0.7689 (m-80) cc_final: 0.7119 (m-80) REVERT: D 58 TYR cc_start: 0.7776 (m-80) cc_final: 0.7386 (m-80) outliers start: 81 outliers final: 50 residues processed: 445 average time/residue: 0.3045 time to fit residues: 210.0661 Evaluate side-chains 392 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 341 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 0.0040 chunk 143 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 174 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 0.0670 chunk 226 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN C 283 GLN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 105 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20744 Z= 0.196 Angle : 0.634 9.844 28157 Z= 0.323 Chirality : 0.045 0.387 3286 Planarity : 0.005 0.049 3579 Dihedral : 5.660 77.092 2874 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.13 % Favored : 94.71 % Rotamer: Outliers : 3.75 % Allowed : 20.06 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2610 helix: 1.31 (0.26), residues: 411 sheet: -0.42 (0.17), residues: 917 loop : -0.99 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 47 HIS 0.005 0.001 HIS E 37 PHE 0.041 0.002 PHE A 483 TYR 0.023 0.001 TYR F 52A ARG 0.006 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 378 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7332 (tttm) REVERT: A 276 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7423 (t0) REVERT: A 448 ASP cc_start: 0.7014 (t0) cc_final: 0.6614 (t0) REVERT: C 448 ASP cc_start: 0.6514 (t0) cc_final: 0.5987 (t0) REVERT: H 100 ASP cc_start: 0.7726 (t0) cc_final: 0.7289 (t0) REVERT: H 100 TYR cc_start: 0.7898 (m-10) cc_final: 0.6975 (m-80) REVERT: H 100 TYR cc_start: 0.7470 (m-80) cc_final: 0.7244 (m-80) REVERT: H 100 TYR cc_start: 0.7701 (m-80) cc_final: 0.7384 (m-80) outliers start: 88 outliers final: 68 residues processed: 435 average time/residue: 0.3014 time to fit residues: 205.3401 Evaluate side-chains 405 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 335 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 105 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20744 Z= 0.186 Angle : 0.625 9.882 28157 Z= 0.318 Chirality : 0.044 0.390 3286 Planarity : 0.004 0.047 3579 Dihedral : 5.500 71.687 2874 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.13 % Favored : 94.71 % Rotamer: Outliers : 4.00 % Allowed : 20.27 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2610 helix: 1.37 (0.26), residues: 411 sheet: -0.38 (0.17), residues: 917 loop : -0.97 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 47 HIS 0.006 0.001 HIS E 37 PHE 0.031 0.002 PHE A 483 TYR 0.024 0.001 TYR F 52A ARG 0.007 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 365 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7411 (tttm) REVERT: A 276 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 448 ASP cc_start: 0.6948 (t0) cc_final: 0.6488 (t0) REVERT: C 448 ASP cc_start: 0.6573 (t0) cc_final: 0.6018 (t0) REVERT: H 100 ASP cc_start: 0.7815 (t0) cc_final: 0.7338 (t0) REVERT: H 100 TYR cc_start: 0.7851 (m-10) cc_final: 0.6894 (m-80) REVERT: H 100 TYR cc_start: 0.7622 (m-80) cc_final: 0.7409 (m-80) outliers start: 94 outliers final: 75 residues processed: 423 average time/residue: 0.3092 time to fit residues: 202.2803 Evaluate side-chains 424 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 347 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 105 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20744 Z= 0.399 Angle : 0.722 10.522 28157 Z= 0.373 Chirality : 0.047 0.402 3286 Planarity : 0.005 0.055 3579 Dihedral : 5.904 68.173 2874 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 5.54 % Allowed : 19.72 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2610 helix: 0.90 (0.26), residues: 432 sheet: -0.62 (0.17), residues: 906 loop : -1.16 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 47 HIS 0.005 0.001 HIS B 159 PHE 0.036 0.002 PHE B 237 TYR 0.029 0.002 TYR F 52A ARG 0.011 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 339 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7088 (ttp80) REVERT: A 97 MET cc_start: 0.7451 (tmm) cc_final: 0.7212 (tmm) REVERT: A 156 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7799 (tttm) REVERT: A 448 ASP cc_start: 0.6980 (t0) cc_final: 0.6616 (t0) REVERT: A 505 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5639 (t80) REVERT: B 49 ARG cc_start: 0.7663 (ttp80) cc_final: 0.6959 (ttp80) REVERT: B 78 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 505 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6109 (t80) REVERT: C 49 ARG cc_start: 0.7818 (ttp80) cc_final: 0.6814 (ttp80) REVERT: C 505 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5467 (t80) REVERT: H 58 TYR cc_start: 0.7661 (m-80) cc_final: 0.7011 (m-80) REVERT: H 100 ASP cc_start: 0.7852 (t0) cc_final: 0.7583 (t0) REVERT: H 100 TYR cc_start: 0.8053 (m-10) cc_final: 0.6944 (m-80) REVERT: H 100 TYR cc_start: 0.7968 (m-80) cc_final: 0.7453 (m-80) REVERT: I 85 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (p) REVERT: D 97 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8659 (mm) outliers start: 130 outliers final: 95 residues processed: 427 average time/residue: 0.3090 time to fit residues: 205.9398 Evaluate side-chains 414 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 312 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 105 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20744 Z= 0.200 Angle : 0.658 14.146 28157 Z= 0.332 Chirality : 0.045 0.385 3286 Planarity : 0.005 0.047 3579 Dihedral : 5.574 62.564 2874 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 4.26 % Allowed : 22.15 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2610 helix: 1.29 (0.26), residues: 411 sheet: -0.52 (0.17), residues: 881 loop : -1.09 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 47 HIS 0.004 0.001 HIS E 37 PHE 0.032 0.002 PHE A 483 TYR 0.029 0.001 TYR F 52A ARG 0.009 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 377 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7540 (tttm) REVERT: A 448 ASP cc_start: 0.6776 (t0) cc_final: 0.6426 (t0) REVERT: A 505 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5693 (t80) REVERT: B 505 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5729 (t80) REVERT: C 417 TYR cc_start: 0.7442 (m-80) cc_final: 0.7040 (m-10) REVERT: C 505 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5608 (t80) REVERT: F 149 PRO cc_start: 0.6017 (Cg_endo) cc_final: 0.5587 (Cg_exo) REVERT: H 58 TYR cc_start: 0.7609 (m-80) cc_final: 0.7146 (m-80) REVERT: H 100 ASP cc_start: 0.7761 (t0) cc_final: 0.7433 (t0) REVERT: H 100 TYR cc_start: 0.7818 (m-10) cc_final: 0.6868 (m-80) REVERT: I 81 GLU cc_start: 0.7318 (pp20) cc_final: 0.7001 (pm20) REVERT: E 106 ILE cc_start: 0.7210 (mm) cc_final: 0.6844 (mm) outliers start: 100 outliers final: 80 residues processed: 438 average time/residue: 0.2981 time to fit residues: 202.7813 Evaluate side-chains 432 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 348 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 234 optimal weight: 0.4980 chunk 240 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 211 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 76 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20744 Z= 0.269 Angle : 0.689 11.999 28157 Z= 0.350 Chirality : 0.046 0.390 3286 Planarity : 0.005 0.054 3579 Dihedral : 5.572 59.513 2874 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Rotamer: Outliers : 4.47 % Allowed : 22.06 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2610 helix: 1.19 (0.26), residues: 411 sheet: -0.51 (0.17), residues: 878 loop : -1.15 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 47 HIS 0.005 0.001 HIS E 37 PHE 0.033 0.002 PHE A 483 TYR 0.030 0.002 TYR F 52A ARG 0.015 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 356 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7581 (tttm) REVERT: A 448 ASP cc_start: 0.6786 (t0) cc_final: 0.6454 (t0) REVERT: A 505 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5614 (t80) REVERT: B 49 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7020 (ttp80) REVERT: B 505 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5751 (t80) REVERT: C 417 TYR cc_start: 0.7603 (m-80) cc_final: 0.6991 (m-10) REVERT: C 505 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5574 (t80) REVERT: F 149 PRO cc_start: 0.6049 (Cg_endo) cc_final: 0.5611 (Cg_exo) REVERT: H 97 ILE cc_start: 0.8902 (mm) cc_final: 0.8566 (tp) REVERT: H 100 TYR cc_start: 0.7975 (m-10) cc_final: 0.6999 (m-80) REVERT: H 100 TYR cc_start: 0.7073 (m-80) cc_final: 0.6607 (m-80) REVERT: E 4 MET cc_start: 0.7279 (mmm) cc_final: 0.6999 (tpp) outliers start: 105 outliers final: 87 residues processed: 426 average time/residue: 0.3273 time to fit residues: 217.5306 Evaluate side-chains 433 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 342 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 247 optimal weight: 0.3980 chunk 151 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 239 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 89 GLN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20744 Z= 0.187 Angle : 0.680 16.709 28157 Z= 0.342 Chirality : 0.045 0.373 3286 Planarity : 0.005 0.049 3579 Dihedral : 5.348 59.425 2874 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 3.45 % Allowed : 23.08 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2610 helix: 1.28 (0.26), residues: 411 sheet: -0.38 (0.17), residues: 892 loop : -1.07 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP H 47 HIS 0.005 0.001 HIS G 37 PHE 0.033 0.002 PHE A 483 TYR 0.029 0.002 TYR F 52A ARG 0.010 0.001 ARG C 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 377 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7508 (tttm) REVERT: A 429 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7506 (tpt-90) REVERT: A 448 ASP cc_start: 0.6857 (t0) cc_final: 0.6392 (t0) REVERT: A 505 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5638 (t80) REVERT: B 49 ARG cc_start: 0.7365 (ttp80) cc_final: 0.6637 (ttp80) REVERT: B 383 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6867 (m-40) REVERT: B 505 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.5797 (t80) REVERT: C 417 TYR cc_start: 0.7184 (m-80) cc_final: 0.6710 (m-10) REVERT: C 505 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.5598 (t80) REVERT: H 58 TYR cc_start: 0.7685 (m-80) cc_final: 0.7247 (m-80) REVERT: H 82 MET cc_start: 0.4232 (mtm) cc_final: 0.3767 (mtm) REVERT: H 97 ILE cc_start: 0.9097 (mm) cc_final: 0.8773 (tp) REVERT: H 100 TYR cc_start: 0.7987 (m-10) cc_final: 0.7089 (m-80) REVERT: H 100 TYR cc_start: 0.7329 (m-80) cc_final: 0.6695 (m-80) REVERT: D 58 TYR cc_start: 0.7760 (m-80) cc_final: 0.7128 (m-80) REVERT: E 4 MET cc_start: 0.7274 (mmm) cc_final: 0.6991 (tpp) REVERT: E 106 ILE cc_start: 0.7191 (mm) cc_final: 0.6936 (mm) outliers start: 81 outliers final: 67 residues processed: 425 average time/residue: 0.3033 time to fit residues: 199.6392 Evaluate side-chains 413 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 341 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 158 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 212 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN F 35 HIS F 76 ASN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS D 76 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110113 restraints weight = 37183.102| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.06 r_work: 0.3349 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20744 Z= 0.247 Angle : 0.682 10.123 28157 Z= 0.348 Chirality : 0.045 0.377 3286 Planarity : 0.005 0.050 3579 Dihedral : 5.355 59.433 2874 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.33 % Rotamer: Outliers : 3.75 % Allowed : 23.51 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2610 helix: 1.24 (0.26), residues: 411 sheet: -0.38 (0.17), residues: 875 loop : -1.08 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP H 36 HIS 0.005 0.001 HIS E 37 PHE 0.033 0.002 PHE A 483 TYR 0.028 0.002 TYR F 52A ARG 0.010 0.001 ARG D 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5143.20 seconds wall clock time: 95 minutes 48.85 seconds (5748.85 seconds total)