Starting phenix.real_space_refine on Sat Mar 16 16:31:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7toe_26030/03_2024/7toe_26030_neut.pdb" } resolution = 3.0 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= 0.012 sd= 0.163 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 80 5.16 5 C 9632 2.51 5 N 2616 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 317": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15100 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 residue: pdb=" N GLU C 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C 504 " occ=0.50 residue: pdb=" N GLU D 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D 504 " occ=0.50 Time building chain proxies: 8.42, per 1000 atoms: 0.56 Number of scatterers: 15100 At special positions: 0 Unit cell: (135.29, 95.45, 117.03, 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 80 16.00 O 2772 8.00 N 2616 7.00 C 9632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.6 seconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 43.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.940A pdb=" N LYS A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.554A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.561A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.638A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.407A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.818A pdb=" N GLU A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.647A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.689A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.891A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.513A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 4.017A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.550A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.799A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.237A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.743A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.601A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.993A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.395A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 4.191A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.695A pdb=" N LYS C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.549A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.272A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.662A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.504A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.041A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.450A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.938A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.700A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.506A pdb=" N LYS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.923A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 4.225A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.614A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.880A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 7.968A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.451A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 7.950A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 421 removed outlier: 6.651A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.317A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.574A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.274A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.620A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1950 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: 4.67 Time building geometry restraints manager: 6.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2647 1.32 - 1.44: 4056 1.44 - 1.57: 8617 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA PRO A 50 " pdb=" CB PRO A 50 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA ILE B 464 " pdb=" C ILE B 464 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.27e-02 6.20e+03 1.38e+01 bond pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.39e-02 5.18e+03 1.05e+01 bond pdb=" C ILE B 464 " pdb=" O ILE B 464 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.19e-02 7.06e+03 9.19e+00 bond pdb=" CA TRP B 462 " pdb=" CB TRP B 462 " ideal model delta sigma weight residual 1.532 1.489 0.044 1.53e-02 4.27e+03 8.14e+00 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.40: 462 106.40 - 113.34: 8104 113.34 - 120.27: 5701 120.27 - 127.21: 6454 127.21 - 134.15: 175 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 310 " pdb=" CA GLY B 310 " pdb=" C GLY B 310 " ideal model delta sigma weight residual 111.36 118.56 -7.20 1.17e+00 7.31e-01 3.79e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 112.35 104.96 7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta sigma weight residual 119.28 113.94 5.34 1.10e+00 8.26e-01 2.36e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 112.38 107.59 4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N TRP B 462 " pdb=" CA TRP B 462 " pdb=" C TRP B 462 " ideal model delta sigma weight residual 113.41 108.66 4.75 1.22e+00 6.72e-01 1.51e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8445 17.87 - 35.74: 683 35.74 - 53.62: 125 53.62 - 71.49: 38 71.49 - 89.36: 13 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N CYS A 158 " pdb=" CA CYS A 158 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER D 157 " pdb=" C SER D 157 " pdb=" N CYS D 158 " pdb=" CA CYS D 158 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 259 " pdb=" C VAL A 259 " pdb=" N MET A 260 " pdb=" CA MET A 260 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1716 0.046 - 0.093: 383 0.093 - 0.139: 139 0.139 - 0.186: 1 0.186 - 0.232: 1 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLN A 119 " pdb=" N GLN A 119 " pdb=" C GLN A 119 " pdb=" CB GLN A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA GLU C 473 " pdb=" N GLU C 473 " pdb=" C GLU C 473 " pdb=" CB GLU C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 312 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 49 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 50 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.020 2.00e-02 2.50e+03 1.75e-02 6.13e+00 pdb=" CG TYR B 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.005 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1218 2.74 - 3.28: 14964 3.28 - 3.82: 25676 3.82 - 4.36: 32498 4.36 - 4.90: 55183 Nonbonded interactions: 129539 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" OE2 GLU A 170 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 139 " pdb=" OH TYR A 437 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR C 139 " pdb=" OH TYR C 437 " model vdw 2.229 2.440 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.232 2.520 nonbonded pdb=" O LYS B 47 " pdb=" OG1 THR B 51 " model vdw 2.234 2.440 ... (remaining 129534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.090 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.850 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.062 15452 Z= 0.209 Angle : 0.588 7.388 20896 Z= 0.327 Chirality : 0.043 0.232 2240 Planarity : 0.004 0.063 2732 Dihedral : 14.035 89.359 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.13 (0.20), residues: 1852 helix: 0.24 (0.20), residues: 704 sheet: -0.60 (0.23), residues: 444 loop : 0.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 225 HIS 0.003 0.001 HIS D 451 PHE 0.021 0.001 PHE C 88 TYR 0.041 0.002 TYR B 139 ARG 0.008 0.000 ARG D 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 1.934 Fit side-chains REVERT: B 30 ASP cc_start: 0.7179 (t0) cc_final: 0.6711 (OUTLIER) REVERT: B 121 LEU cc_start: 0.8476 (tt) cc_final: 0.8273 (tm) REVERT: B 130 LEU cc_start: 0.8312 (tp) cc_final: 0.8079 (tp) REVERT: B 171 LYS cc_start: 0.7717 (ptmm) cc_final: 0.7397 (pttp) REVERT: B 249 TYR cc_start: 0.7017 (t80) cc_final: 0.6789 (t80) REVERT: B 446 CYS cc_start: 0.7767 (m) cc_final: 0.7461 (m) REVERT: B 497 LYS cc_start: 0.8358 (tptt) cc_final: 0.7998 (tttp) REVERT: D 37 MET cc_start: 0.8817 (mmm) cc_final: 0.8563 (mmt) REVERT: D 140 LEU cc_start: 0.8260 (mp) cc_final: 0.8015 (mt) outliers start: 2 outliers final: 3 residues processed: 292 average time/residue: 1.1842 time to fit residues: 383.1625 Evaluate side-chains 189 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 167 optimal weight: 0.0870 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 64 ASN D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15452 Z= 0.185 Angle : 0.555 8.254 20896 Z= 0.289 Chirality : 0.044 0.206 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.520 64.586 2060 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 9.50 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.20), residues: 1852 helix: 0.57 (0.21), residues: 692 sheet: -0.50 (0.24), residues: 408 loop : -0.14 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 225 HIS 0.004 0.001 HIS A 124 PHE 0.018 0.001 PHE C 241 TYR 0.020 0.001 TYR A 308 ARG 0.006 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.678 Fit side-chains REVERT: B 30 ASP cc_start: 0.7110 (t0) cc_final: 0.6664 (OUTLIER) REVERT: B 97 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7331 (ttpt) REVERT: B 130 LEU cc_start: 0.8304 (tp) cc_final: 0.8056 (tp) REVERT: B 171 LYS cc_start: 0.7716 (ptmm) cc_final: 0.7419 (pttp) REVERT: B 249 TYR cc_start: 0.6970 (t80) cc_final: 0.6735 (t80) REVERT: B 389 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: B 395 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: B 446 CYS cc_start: 0.7667 (m) cc_final: 0.7442 (m) REVERT: B 497 LYS cc_start: 0.8331 (tptt) cc_final: 0.7959 (tttp) REVERT: C 130 LEU cc_start: 0.8557 (tp) cc_final: 0.7899 (tm) REVERT: C 405 MET cc_start: 0.7917 (mmm) cc_final: 0.7062 (mmt) REVERT: D 37 MET cc_start: 0.8745 (mmm) cc_final: 0.8319 (mmt) REVERT: D 95 LYS cc_start: 0.7674 (tmmt) cc_final: 0.7336 (mtpm) REVERT: D 135 ASN cc_start: 0.8308 (m-40) cc_final: 0.7897 (m110) outliers start: 24 outliers final: 12 residues processed: 228 average time/residue: 1.0940 time to fit residues: 280.4651 Evaluate side-chains 198 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 180 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS D 414 ASN D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15452 Z= 0.323 Angle : 0.597 7.432 20896 Z= 0.304 Chirality : 0.045 0.158 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.422 19.446 2056 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 2.45 % Allowed : 12.38 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.31 (0.20), residues: 1852 helix: 0.22 (0.19), residues: 748 sheet: -0.72 (0.24), residues: 412 loop : -0.08 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 53 HIS 0.005 0.001 HIS A 124 PHE 0.016 0.002 PHE B 102 TYR 0.020 0.002 TYR B 139 ARG 0.007 0.001 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.658 Fit side-chains REVERT: A 258 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7682 (t70) REVERT: B 97 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7153 (ttpp) REVERT: B 249 TYR cc_start: 0.7049 (t80) cc_final: 0.6811 (t80) REVERT: B 280 ASN cc_start: 0.7825 (m-40) cc_final: 0.7487 (m-40) REVERT: B 389 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 395 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: B 446 CYS cc_start: 0.7795 (m) cc_final: 0.7496 (m) REVERT: B 497 LYS cc_start: 0.8343 (tptt) cc_final: 0.7962 (tttp) REVERT: C 411 MET cc_start: 0.7655 (mpt) cc_final: 0.6871 (mpt) REVERT: C 475 GLU cc_start: 0.8019 (tt0) cc_final: 0.7743 (tm-30) REVERT: D 37 MET cc_start: 0.8714 (mmm) cc_final: 0.8039 (mmt) REVERT: D 66 PHE cc_start: 0.8154 (m-80) cc_final: 0.7890 (m-80) REVERT: D 135 ASN cc_start: 0.8352 (m-40) cc_final: 0.7911 (m110) outliers start: 40 outliers final: 22 residues processed: 224 average time/residue: 1.1048 time to fit residues: 275.8465 Evaluate side-chains 211 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 0.0970 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15452 Z= 0.214 Angle : 0.544 7.235 20896 Z= 0.279 Chirality : 0.043 0.183 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.319 20.200 2056 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 14.34 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.17 (0.20), residues: 1852 helix: 0.47 (0.20), residues: 724 sheet: -0.72 (0.24), residues: 408 loop : -0.10 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.005 0.001 HIS A 124 PHE 0.019 0.001 PHE C 88 TYR 0.019 0.001 TYR A 308 ARG 0.007 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.704 Fit side-chains REVERT: A 258 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7666 (t70) REVERT: B 130 LEU cc_start: 0.8396 (tp) cc_final: 0.8160 (tp) REVERT: B 249 TYR cc_start: 0.6988 (t80) cc_final: 0.6742 (t80) REVERT: B 280 ASN cc_start: 0.7799 (m-40) cc_final: 0.7459 (m-40) REVERT: B 389 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: B 395 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: B 446 CYS cc_start: 0.7773 (m) cc_final: 0.7474 (m) REVERT: B 497 LYS cc_start: 0.8317 (tptt) cc_final: 0.7950 (tttp) REVERT: C 130 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8124 (tt) REVERT: C 475 GLU cc_start: 0.7974 (tt0) cc_final: 0.7713 (tm-30) REVERT: D 37 MET cc_start: 0.8714 (mmm) cc_final: 0.8006 (mmt) REVERT: D 135 ASN cc_start: 0.8306 (m-40) cc_final: 0.7968 (m110) outliers start: 32 outliers final: 18 residues processed: 216 average time/residue: 1.1301 time to fit residues: 272.3829 Evaluate side-chains 201 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN C 105 ASN C 451 HIS D 266 GLN D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15452 Z= 0.431 Angle : 0.648 8.073 20896 Z= 0.329 Chirality : 0.046 0.184 2240 Planarity : 0.005 0.052 2732 Dihedral : 4.634 21.625 2056 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 2.70 % Allowed : 15.81 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.43 (0.20), residues: 1852 helix: 0.12 (0.19), residues: 744 sheet: -0.91 (0.23), residues: 440 loop : 0.00 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 164 HIS 0.006 0.001 HIS C 470 PHE 0.020 0.002 PHE A 413 TYR 0.017 0.002 TYR A 308 ARG 0.008 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7609 (ptm160) REVERT: A 258 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7716 (t70) REVERT: B 249 TYR cc_start: 0.7062 (t80) cc_final: 0.6840 (t80) REVERT: B 280 ASN cc_start: 0.7891 (m-40) cc_final: 0.7568 (m-40) REVERT: B 389 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: B 395 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: B 446 CYS cc_start: 0.7844 (m) cc_final: 0.7469 (m) REVERT: B 497 LYS cc_start: 0.8364 (tptt) cc_final: 0.7985 (tttp) REVERT: C 89 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8416 (mptt) REVERT: C 120 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8092 (ptp90) REVERT: C 130 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8215 (tt) REVERT: C 405 MET cc_start: 0.7848 (mmm) cc_final: 0.7440 (mmm) REVERT: C 475 GLU cc_start: 0.8047 (tt0) cc_final: 0.7756 (tm-30) REVERT: D 37 MET cc_start: 0.8709 (mmm) cc_final: 0.7971 (mmt) REVERT: D 66 PHE cc_start: 0.8145 (m-80) cc_final: 0.7930 (m-80) REVERT: D 99 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 135 ASN cc_start: 0.8405 (m-40) cc_final: 0.7909 (m110) REVERT: D 140 LEU cc_start: 0.8103 (mp) cc_final: 0.7886 (mt) outliers start: 44 outliers final: 24 residues processed: 240 average time/residue: 1.1245 time to fit residues: 300.7106 Evaluate side-chains 217 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 266 GLN D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15452 Z= 0.246 Angle : 0.572 8.412 20896 Z= 0.291 Chirality : 0.044 0.196 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.481 20.379 2056 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 2.70 % Allowed : 17.46 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.36 (0.20), residues: 1852 helix: 0.25 (0.19), residues: 748 sheet: -0.98 (0.22), residues: 452 loop : 0.05 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 164 HIS 0.004 0.001 HIS A 124 PHE 0.020 0.001 PHE C 88 TYR 0.021 0.001 TYR A 308 ARG 0.007 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: A 120 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7657 (ttp80) REVERT: A 176 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: A 258 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7683 (t70) REVERT: B 258 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: B 280 ASN cc_start: 0.7855 (m-40) cc_final: 0.7545 (m-40) REVERT: B 389 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: B 395 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: B 446 CYS cc_start: 0.7788 (m) cc_final: 0.7430 (m) REVERT: B 497 LYS cc_start: 0.8299 (tptt) cc_final: 0.7933 (tttp) REVERT: C 89 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8415 (mptt) REVERT: C 120 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8186 (ptp90) REVERT: C 130 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8176 (tt) REVERT: C 405 MET cc_start: 0.7895 (mmm) cc_final: 0.7367 (mmm) REVERT: C 475 GLU cc_start: 0.7973 (tt0) cc_final: 0.7717 (tm-30) REVERT: D 37 MET cc_start: 0.8706 (mmm) cc_final: 0.7978 (mmt) REVERT: D 66 PHE cc_start: 0.8123 (m-80) cc_final: 0.7907 (m-80) REVERT: D 135 ASN cc_start: 0.8345 (m-40) cc_final: 0.7911 (m110) outliers start: 44 outliers final: 22 residues processed: 231 average time/residue: 1.1662 time to fit residues: 299.4417 Evaluate side-chains 218 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15452 Z= 0.380 Angle : 0.624 11.105 20896 Z= 0.316 Chirality : 0.046 0.193 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.589 21.927 2056 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.94 % Allowed : 18.32 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.49 (0.19), residues: 1852 helix: 0.14 (0.19), residues: 740 sheet: -1.05 (0.22), residues: 452 loop : 0.01 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 164 HIS 0.005 0.001 HIS C 470 PHE 0.021 0.002 PHE C 102 TYR 0.020 0.002 TYR A 308 ARG 0.007 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8000 (pt0) REVERT: A 120 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7648 (ttp80) REVERT: A 258 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7714 (t70) REVERT: B 130 LEU cc_start: 0.8457 (tp) cc_final: 0.8218 (tm) REVERT: B 258 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: B 280 ASN cc_start: 0.7883 (m-40) cc_final: 0.7561 (m-40) REVERT: B 389 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: B 395 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: B 446 CYS cc_start: 0.7836 (m) cc_final: 0.7467 (m) REVERT: B 497 LYS cc_start: 0.8313 (tptt) cc_final: 0.7946 (tttp) REVERT: C 89 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8451 (mptt) REVERT: C 120 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7977 (ptp90) REVERT: C 130 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 356 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 405 MET cc_start: 0.7953 (mmm) cc_final: 0.7309 (mmm) REVERT: C 475 GLU cc_start: 0.8050 (tt0) cc_final: 0.7741 (tm-30) REVERT: D 37 MET cc_start: 0.8707 (mmm) cc_final: 0.7988 (mmt) REVERT: D 66 PHE cc_start: 0.8104 (m-80) cc_final: 0.7612 (m-80) REVERT: D 135 ASN cc_start: 0.8371 (m-40) cc_final: 0.7931 (m110) outliers start: 48 outliers final: 25 residues processed: 231 average time/residue: 1.1349 time to fit residues: 291.8484 Evaluate side-chains 214 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 266 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15452 Z= 0.179 Angle : 0.545 10.357 20896 Z= 0.277 Chirality : 0.042 0.192 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.341 20.699 2056 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 2.39 % Allowed : 18.75 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.18 (0.20), residues: 1852 helix: 0.51 (0.20), residues: 724 sheet: -0.89 (0.23), residues: 416 loop : -0.05 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 PHE 0.027 0.001 PHE C 56 TYR 0.021 0.001 TYR A 308 ARG 0.009 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: A 120 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7647 (ttp80) REVERT: A 159 MET cc_start: 0.7670 (tpp) cc_final: 0.7463 (tpp) REVERT: A 258 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: B 88 PHE cc_start: 0.8072 (m-80) cc_final: 0.7393 (m-80) REVERT: B 130 LEU cc_start: 0.8446 (tp) cc_final: 0.8236 (tm) REVERT: B 258 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: B 395 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: B 446 CYS cc_start: 0.7709 (m) cc_final: 0.7414 (m) REVERT: B 497 LYS cc_start: 0.8231 (tptt) cc_final: 0.7860 (tttp) REVERT: C 89 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8446 (mptt) REVERT: C 120 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8073 (ptp90) REVERT: C 130 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8164 (tt) REVERT: C 356 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 475 GLU cc_start: 0.7998 (tt0) cc_final: 0.7684 (tm-30) REVERT: D 37 MET cc_start: 0.8721 (mmm) cc_final: 0.8065 (mmt) REVERT: D 66 PHE cc_start: 0.8095 (m-80) cc_final: 0.7632 (m-80) REVERT: D 99 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: D 135 ASN cc_start: 0.8303 (m-40) cc_final: 0.7920 (m110) outliers start: 39 outliers final: 18 residues processed: 224 average time/residue: 1.0790 time to fit residues: 270.1238 Evaluate side-chains 215 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 0.0980 chunk 165 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15452 Z= 0.209 Angle : 0.555 10.372 20896 Z= 0.280 Chirality : 0.043 0.196 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.293 20.136 2056 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.33 % Allowed : 19.18 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1852 helix: 0.60 (0.20), residues: 720 sheet: -0.90 (0.23), residues: 452 loop : -0.00 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 53 HIS 0.005 0.001 HIS D 451 PHE 0.028 0.001 PHE C 56 TYR 0.023 0.001 TYR C 147 ARG 0.009 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: A 120 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7653 (ttp80) REVERT: A 258 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: A 470 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7788 (m-70) REVERT: B 88 PHE cc_start: 0.8046 (m-80) cc_final: 0.7393 (m-80) REVERT: B 130 LEU cc_start: 0.8438 (tp) cc_final: 0.8228 (tm) REVERT: B 258 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: B 395 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7191 (pt0) REVERT: B 446 CYS cc_start: 0.7710 (m) cc_final: 0.7430 (m) REVERT: B 497 LYS cc_start: 0.8223 (tptt) cc_final: 0.7673 (mptt) REVERT: C 89 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8427 (mptt) REVERT: C 120 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8198 (ptp90) REVERT: C 130 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8107 (tt) REVERT: C 356 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 475 GLU cc_start: 0.7981 (tt0) cc_final: 0.7681 (tm-30) REVERT: D 37 MET cc_start: 0.8745 (mmm) cc_final: 0.8193 (mmt) REVERT: D 66 PHE cc_start: 0.8012 (m-80) cc_final: 0.7516 (m-80) REVERT: D 95 LYS cc_start: 0.7587 (tmmt) cc_final: 0.6998 (mtpm) REVERT: D 99 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: D 135 ASN cc_start: 0.8274 (m-40) cc_final: 0.7946 (m110) outliers start: 38 outliers final: 21 residues processed: 225 average time/residue: 1.1186 time to fit residues: 281.0250 Evaluate side-chains 221 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 ASN C 83 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 229 ASN D 266 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15452 Z= 0.372 Angle : 0.642 11.780 20896 Z= 0.322 Chirality : 0.045 0.221 2240 Planarity : 0.005 0.068 2732 Dihedral : 4.595 20.499 2056 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 2.08 % Allowed : 19.67 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.42 (0.19), residues: 1852 helix: 0.28 (0.19), residues: 736 sheet: -1.04 (0.22), residues: 452 loop : -0.05 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.032 0.002 PHE C 56 TYR 0.021 0.002 TYR C 147 ARG 0.014 0.001 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: A 120 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7665 (ttp80) REVERT: A 176 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: A 258 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7741 (t70) REVERT: B 88 PHE cc_start: 0.8092 (m-80) cc_final: 0.7429 (m-80) REVERT: B 258 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: B 280 ASN cc_start: 0.7890 (m-40) cc_final: 0.7571 (m-40) REVERT: B 319 THR cc_start: 0.8967 (t) cc_final: 0.8712 (p) REVERT: B 446 CYS cc_start: 0.7812 (m) cc_final: 0.7452 (m) REVERT: C 80 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 89 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8442 (mptt) REVERT: C 120 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8058 (ptp90) REVERT: C 130 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 356 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 475 GLU cc_start: 0.7996 (tt0) cc_final: 0.7706 (tm-30) REVERT: D 37 MET cc_start: 0.8722 (mmm) cc_final: 0.8165 (mmt) REVERT: D 66 PHE cc_start: 0.8010 (m-80) cc_final: 0.7512 (m-80) REVERT: D 95 LYS cc_start: 0.7652 (tmmt) cc_final: 0.7150 (mtpm) REVERT: D 135 ASN cc_start: 0.8307 (m-40) cc_final: 0.7994 (m110) outliers start: 34 outliers final: 22 residues processed: 218 average time/residue: 1.0778 time to fit residues: 264.1550 Evaluate side-chains 215 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122743 restraints weight = 17861.708| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.19 r_work: 0.3320 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15452 Z= 0.191 Angle : 0.570 15.271 20896 Z= 0.286 Chirality : 0.043 0.220 2240 Planarity : 0.004 0.059 2732 Dihedral : 4.378 19.711 2056 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.59 % Allowed : 20.40 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.17 (0.20), residues: 1852 helix: 0.61 (0.20), residues: 712 sheet: -0.93 (0.23), residues: 452 loop : -0.04 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.035 0.001 PHE C 56 TYR 0.022 0.001 TYR A 308 ARG 0.013 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.30 seconds wall clock time: 93 minutes 35.77 seconds (5615.77 seconds total)