Starting phenix.real_space_refine on Wed Feb 14 19:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk2_34842/02_2024/8hk2_34842_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 517 atoms to isotropic. 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 76 5.16 5 C 6134 2.51 5 N 1609 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9548 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2234 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2580 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 553 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 438 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 176 Unusual residues: {'CLR': 5, 'PLM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.64, per 1000 atoms: 0.59 Number of scatterers: 9548 At special positions: 0 Unit cell: (107.12, 115.36, 150.792, 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 76 16.00 O 1729 8.00 N 1609 7.00 C 6134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " distance=1.69 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.09 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 56 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.8 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 36.3% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 56 through 83 removed outlier: 3.655A pdb=" N TRP A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 94 through 125 Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.613A pdb=" N ASN A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 346 through 364 Processing helix chain 'A' and resid 374 through 401 Proline residue: A 392 - end of helix removed outlier: 3.511A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 435 removed outlier: 3.974A pdb=" N HIS A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'B' and resid 7 through 31 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.785A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 271 through 280 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 296 through 310 removed outlier: 3.830A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.263A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 49 through 71 removed outlier: 3.600A pdb=" N HIS D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 162 through 166 removed outlier: 3.828A pdb=" N HIS A 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 319 through 323 removed outlier: 7.645A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 189 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 198 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 187 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 200 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.046A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.718A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 123 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 178 through 180 Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.723A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.602A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 276 through 278 removed outlier: 4.126A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.694A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'H' and resid 93 through 99 removed outlier: 5.667A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.509A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'H' and resid 226 through 231 removed outlier: 3.664A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1547 1.32 - 1.45: 2653 1.45 - 1.58: 5445 1.58 - 1.71: 0 1.71 - 1.83: 107 Bond restraints: 9752 Sorted by residual: bond pdb=" CA SER D 35 " pdb=" C SER D 35 " ideal model delta sigma weight residual 1.523 1.433 0.090 1.34e-02 5.57e+03 4.51e+01 bond pdb=" CA ASN D 30 " pdb=" C ASN D 30 " ideal model delta sigma weight residual 1.525 1.456 0.069 1.04e-02 9.25e+03 4.41e+01 bond pdb=" CA ARG B 21 " pdb=" C ARG B 21 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.24e-02 6.50e+03 3.85e+01 bond pdb=" CA ARG D 64 " pdb=" C ARG D 64 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.39e-02 5.18e+03 3.10e+01 bond pdb=" CA GLU D 29 " pdb=" C GLU D 29 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.38e-02 5.25e+03 2.99e+01 ... (remaining 9747 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.92: 212 105.92 - 113.00: 5297 113.00 - 120.07: 3367 120.07 - 127.14: 4242 127.14 - 134.22: 108 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N GLN D 3 " pdb=" CA GLN D 3 " pdb=" C GLN D 3 " ideal model delta sigma weight residual 112.54 98.85 13.69 1.22e+00 6.72e-01 1.26e+02 angle pdb=" N ARG D 64 " pdb=" CA ARG D 64 " pdb=" C ARG D 64 " ideal model delta sigma weight residual 112.89 102.64 10.25 1.24e+00 6.50e-01 6.83e+01 angle pdb=" N PRO D 31 " pdb=" CA PRO D 31 " pdb=" C PRO D 31 " ideal model delta sigma weight residual 113.57 103.08 10.49 1.31e+00 5.83e-01 6.41e+01 angle pdb=" N THR D 5 " pdb=" CA THR D 5 " pdb=" C THR D 5 " ideal model delta sigma weight residual 111.36 102.75 8.61 1.09e+00 8.42e-01 6.24e+01 angle pdb=" N CYS C 148 " pdb=" CA CYS C 148 " pdb=" C CYS C 148 " ideal model delta sigma weight residual 108.13 119.72 -11.59 1.72e+00 3.38e-01 4.54e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 5829 18.33 - 36.66: 173 36.66 - 54.98: 30 54.98 - 73.31: 10 73.31 - 91.64: 2 Dihedral angle restraints: 6044 sinusoidal: 2538 harmonic: 3506 Sorted by residual: dihedral pdb=" C PHE D 34 " pdb=" N PHE D 34 " pdb=" CA PHE D 34 " pdb=" CB PHE D 34 " ideal model delta harmonic sigma weight residual -122.60 -143.57 20.97 0 2.50e+00 1.60e-01 7.03e+01 dihedral pdb=" N PHE D 34 " pdb=" C PHE D 34 " pdb=" CA PHE D 34 " pdb=" CB PHE D 34 " ideal model delta harmonic sigma weight residual 122.80 142.89 -20.09 0 2.50e+00 1.60e-01 6.46e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 150.30 -57.30 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 6041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 1493 0.190 - 0.380: 26 0.380 - 0.570: 4 0.570 - 0.761: 0 0.761 - 0.951: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CA PHE D 34 " pdb=" N PHE D 34 " pdb=" C PHE D 34 " pdb=" CB PHE D 34 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" CA LEU D 63 " pdb=" N LEU D 63 " pdb=" C LEU D 63 " pdb=" CB LEU D 63 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA CYS A 172 " pdb=" N CYS A 172 " pdb=" C CYS A 172 " pdb=" CB CYS A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 1522 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 94 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LEU A 94 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU A 94 " -0.031 2.00e-02 2.50e+03 pdb=" N CYS A 95 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 6 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C GLN C 6 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN C 6 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C 7 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 230 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C MET H 230 " 0.058 2.00e-02 2.50e+03 pdb=" O MET H 230 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN H 231 " -0.020 2.00e-02 2.50e+03 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 169 2.67 - 3.23: 8354 3.23 - 3.79: 14612 3.79 - 4.34: 19507 4.34 - 4.90: 32670 Nonbonded interactions: 75312 Sorted by model distance: nonbonded pdb=" NZ LYS A 96 " pdb=" O ARG A 161 " model vdw 2.114 2.520 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.235 2.440 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR H 175 " model vdw 2.242 2.440 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.265 2.440 nonbonded pdb=" O THR A 165 " pdb=" OG1 THR A 165 " model vdw 2.272 2.440 ... (remaining 75307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:12.780 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.007 0.097 9752 Z= 0.433 Angle : 1.060 13.693 13226 Z= 0.618 Chirality : 0.076 0.951 1525 Planarity : 0.007 0.055 1634 Dihedral : 9.701 91.640 3764 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer: Outliers : 0.79 % Allowed : 2.87 % Favored : 96.34 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1190 helix: 1.62 (0.24), residues: 465 sheet: 0.52 (0.29), residues: 306 loop : -1.35 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 111 HIS 0.007 0.002 HIS A 133 PHE 0.038 0.003 PHE A 396 TYR 0.016 0.002 TYR H 190 ARG 0.006 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 299 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8681 (tt) cc_final: 0.8471 (tm) REVERT: A 433 PHE cc_start: 0.8735 (m-80) cc_final: 0.8523 (m-80) REVERT: B 261 ASP cc_start: 0.6925 (t70) cc_final: 0.6698 (t0) REVERT: B 295 THR cc_start: 0.8142 (m) cc_final: 0.7932 (p) REVERT: C 74 SER cc_start: 0.7764 (p) cc_final: 0.7339 (p) REVERT: C 258 ASP cc_start: 0.7317 (t0) cc_final: 0.7072 (t0) REVERT: H 223 ASP cc_start: 0.8225 (m-30) cc_final: 0.7959 (m-30) REVERT: H 238 THR cc_start: 0.8876 (m) cc_final: 0.8635 (p) outliers start: 8 outliers final: 6 residues processed: 304 average time/residue: 1.0942 time to fit residues: 356.9121 Evaluate side-chains 231 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 244 HIS B 269 ASN C 32 GLN C 88 ASN C 142 HIS C 155 ASN C 176 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9752 Z= 0.215 Angle : 0.559 9.047 13226 Z= 0.288 Chirality : 0.041 0.136 1525 Planarity : 0.004 0.049 1634 Dihedral : 6.031 59.846 1663 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.34 % Favored : 98.57 % Rotamer: Outliers : 3.96 % Allowed : 14.55 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1190 helix: 2.48 (0.24), residues: 454 sheet: 0.71 (0.29), residues: 305 loop : -1.04 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS C 142 PHE 0.015 0.002 PHE H 27 TYR 0.011 0.001 TYR H 190 ARG 0.007 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8732 (mm) cc_final: 0.8523 (mm) REVERT: A 171 ARG cc_start: 0.6804 (mtt-85) cc_final: 0.6545 (mtt-85) REVERT: A 340 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.6965 (ttp-170) REVERT: A 433 PHE cc_start: 0.8828 (m-80) cc_final: 0.8590 (m-80) REVERT: B 197 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7871 (mmtp) REVERT: B 261 ASP cc_start: 0.6924 (t70) cc_final: 0.6666 (t0) REVERT: B 295 THR cc_start: 0.8241 (m) cc_final: 0.7992 (p) REVERT: C 327 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (p) REVERT: D 63 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8301 (tm) outliers start: 40 outliers final: 14 residues processed: 253 average time/residue: 1.1196 time to fit residues: 304.6698 Evaluate side-chains 238 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 176 GLN C 230 ASN H 82 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 9752 Z= 0.475 Angle : 0.677 9.997 13226 Z= 0.347 Chirality : 0.046 0.148 1525 Planarity : 0.005 0.050 1634 Dihedral : 6.281 55.340 1661 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 5.35 % Allowed : 15.15 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1190 helix: 1.85 (0.24), residues: 469 sheet: 0.56 (0.29), residues: 305 loop : -1.21 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 82 HIS 0.010 0.002 HIS B 188 PHE 0.019 0.003 PHE A 125 TYR 0.017 0.002 TYR H 190 ARG 0.008 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 239 time to evaluate : 1.020 Fit side-chains REVERT: A 27 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: A 340 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7059 (ttp-170) REVERT: A 433 PHE cc_start: 0.8831 (m-80) cc_final: 0.8579 (m-80) REVERT: A 443 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7898 (ttp80) REVERT: B 240 MET cc_start: 0.5664 (pp-130) cc_final: 0.5136 (pp-130) REVERT: B 261 ASP cc_start: 0.7025 (t70) cc_final: 0.6712 (t0) REVERT: B 278 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 295 THR cc_start: 0.8388 (m) cc_final: 0.8105 (p) REVERT: C 258 ASP cc_start: 0.7382 (t0) cc_final: 0.7055 (t0) REVERT: D 63 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8397 (tm) REVERT: G 30 VAL cc_start: 0.8987 (t) cc_final: 0.8779 (t) outliers start: 54 outliers final: 28 residues processed: 263 average time/residue: 1.1844 time to fit residues: 333.2820 Evaluate side-chains 262 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.0570 chunk 107 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 75 GLN C 176 GLN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9752 Z= 0.167 Angle : 0.545 8.166 13226 Z= 0.271 Chirality : 0.039 0.138 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.560 59.039 1661 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.18 % Favored : 98.74 % Rotamer: Outliers : 3.86 % Allowed : 18.51 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1190 helix: 2.16 (0.25), residues: 468 sheet: 0.78 (0.29), residues: 303 loop : -1.01 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS A 169 PHE 0.021 0.002 PHE B 354 TYR 0.009 0.001 TYR H 190 ARG 0.015 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: A 35 LEU cc_start: 0.8749 (mm) cc_final: 0.8546 (mm) REVERT: A 433 PHE cc_start: 0.8805 (m-80) cc_final: 0.8538 (m-80) REVERT: A 443 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7862 (ttp80) REVERT: B 261 ASP cc_start: 0.6958 (t70) cc_final: 0.6661 (t0) REVERT: B 295 THR cc_start: 0.8382 (m) cc_final: 0.8096 (p) REVERT: C 258 ASP cc_start: 0.7351 (t70) cc_final: 0.6992 (t0) REVERT: H 5 VAL cc_start: 0.8305 (t) cc_final: 0.8059 (p) REVERT: H 91 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8410 (p) REVERT: H 139 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8742 (t) outliers start: 39 outliers final: 16 residues processed: 246 average time/residue: 1.1567 time to fit residues: 304.9099 Evaluate side-chains 243 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9752 Z= 0.205 Angle : 0.542 8.734 13226 Z= 0.271 Chirality : 0.040 0.132 1525 Planarity : 0.004 0.057 1634 Dihedral : 5.187 49.419 1658 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.85 % Favored : 98.07 % Rotamer: Outliers : 3.86 % Allowed : 19.90 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1190 helix: 2.14 (0.24), residues: 472 sheet: 0.74 (0.29), residues: 300 loop : -0.86 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 PHE 0.030 0.002 PHE B 354 TYR 0.011 0.001 TYR H 190 ARG 0.016 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 234 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7203 (mpp) REVERT: A 35 LEU cc_start: 0.8747 (mm) cc_final: 0.8541 (mm) REVERT: A 433 PHE cc_start: 0.8810 (m-80) cc_final: 0.8572 (m-80) REVERT: A 443 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7898 (ttp80) REVERT: B 261 ASP cc_start: 0.6954 (t70) cc_final: 0.6665 (t0) REVERT: B 295 THR cc_start: 0.8385 (m) cc_final: 0.8068 (p) REVERT: C 258 ASP cc_start: 0.7366 (t70) cc_final: 0.7002 (t0) REVERT: D 28 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7444 (mmt90) REVERT: H 5 VAL cc_start: 0.8314 (t) cc_final: 0.8077 (p) outliers start: 39 outliers final: 25 residues processed: 254 average time/residue: 1.1019 time to fit residues: 300.4725 Evaluate side-chains 247 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS C 176 GLN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9752 Z= 0.292 Angle : 0.575 9.083 13226 Z= 0.289 Chirality : 0.041 0.135 1525 Planarity : 0.004 0.046 1634 Dihedral : 5.384 51.694 1658 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 4.46 % Allowed : 19.21 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1190 helix: 2.08 (0.24), residues: 470 sheet: 0.62 (0.29), residues: 297 loop : -0.89 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS B 213 PHE 0.030 0.002 PHE B 354 TYR 0.013 0.001 TYR H 190 ARG 0.009 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7201 (mpp) REVERT: A 35 LEU cc_start: 0.8769 (mm) cc_final: 0.8553 (mm) REVERT: A 433 PHE cc_start: 0.8812 (m-80) cc_final: 0.8570 (m-80) REVERT: A 443 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7932 (ttp80) REVERT: B 261 ASP cc_start: 0.6976 (t70) cc_final: 0.6692 (t0) REVERT: B 295 THR cc_start: 0.8438 (m) cc_final: 0.8106 (p) REVERT: C 258 ASP cc_start: 0.7385 (t70) cc_final: 0.7042 (t0) REVERT: H 5 VAL cc_start: 0.8362 (t) cc_final: 0.8147 (p) outliers start: 45 outliers final: 25 residues processed: 253 average time/residue: 1.1630 time to fit residues: 315.7782 Evaluate side-chains 250 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 83 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 75 GLN C 119 ASN C 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9752 Z= 0.138 Angle : 0.541 9.776 13226 Z= 0.265 Chirality : 0.039 0.135 1525 Planarity : 0.004 0.051 1634 Dihedral : 4.938 51.509 1658 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 2.77 % Allowed : 21.09 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1190 helix: 2.40 (0.24), residues: 463 sheet: 0.67 (0.29), residues: 299 loop : -0.68 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS A 169 PHE 0.026 0.001 PHE B 354 TYR 0.011 0.001 TYR A 160 ARG 0.017 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7182 (mpp) REVERT: A 35 LEU cc_start: 0.8735 (mm) cc_final: 0.8507 (mm) REVERT: A 433 PHE cc_start: 0.8800 (m-80) cc_final: 0.8589 (m-80) REVERT: A 435 TYR cc_start: 0.8749 (m-80) cc_final: 0.8537 (m-80) REVERT: B 261 ASP cc_start: 0.6915 (t70) cc_final: 0.6634 (t0) REVERT: B 295 THR cc_start: 0.8428 (m) cc_final: 0.8076 (p) REVERT: C 258 ASP cc_start: 0.7360 (t70) cc_final: 0.7018 (t0) REVERT: D 28 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7323 (mmt90) REVERT: H 5 VAL cc_start: 0.8234 (t) cc_final: 0.8002 (p) REVERT: H 91 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8436 (p) outliers start: 28 outliers final: 17 residues processed: 240 average time/residue: 1.1283 time to fit residues: 290.7141 Evaluate side-chains 238 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 72 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN C 237 ASN D 37 GLN H 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9752 Z= 0.154 Angle : 0.535 8.497 13226 Z= 0.263 Chirality : 0.039 0.134 1525 Planarity : 0.003 0.045 1634 Dihedral : 4.837 52.491 1658 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 20.30 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1190 helix: 2.44 (0.25), residues: 463 sheet: 0.68 (0.29), residues: 299 loop : -0.65 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS A 169 PHE 0.031 0.001 PHE B 354 TYR 0.009 0.001 TYR C 111 ARG 0.011 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8728 (mm) cc_final: 0.8494 (mm) REVERT: A 433 PHE cc_start: 0.8813 (m-80) cc_final: 0.8583 (m-80) REVERT: A 443 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7981 (ttp80) REVERT: B 261 ASP cc_start: 0.6910 (t70) cc_final: 0.6627 (t0) REVERT: B 295 THR cc_start: 0.8454 (m) cc_final: 0.8089 (p) REVERT: C 61 MET cc_start: 0.8481 (tmm) cc_final: 0.8280 (ppp) REVERT: C 258 ASP cc_start: 0.7330 (t70) cc_final: 0.7015 (t0) REVERT: H 5 VAL cc_start: 0.8253 (t) cc_final: 0.8006 (p) REVERT: H 91 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8439 (p) outliers start: 33 outliers final: 16 residues processed: 243 average time/residue: 1.1406 time to fit residues: 297.1639 Evaluate side-chains 239 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN C 230 ASN H 77 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9752 Z= 0.212 Angle : 0.564 8.315 13226 Z= 0.281 Chirality : 0.040 0.133 1525 Planarity : 0.003 0.048 1634 Dihedral : 4.777 34.919 1656 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.15 % Rotamer: Outliers : 3.17 % Allowed : 20.99 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1190 helix: 2.40 (0.25), residues: 464 sheet: 0.55 (0.29), residues: 305 loop : -0.73 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 PHE 0.031 0.002 PHE B 354 TYR 0.012 0.001 TYR H 190 ARG 0.009 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8736 (mm) cc_final: 0.8521 (mm) REVERT: A 443 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: B 261 ASP cc_start: 0.6940 (t70) cc_final: 0.6668 (t0) REVERT: B 295 THR cc_start: 0.8471 (m) cc_final: 0.8111 (p) REVERT: C 258 ASP cc_start: 0.7331 (t70) cc_final: 0.7007 (t0) REVERT: H 5 VAL cc_start: 0.8293 (t) cc_final: 0.8060 (p) outliers start: 32 outliers final: 21 residues processed: 246 average time/residue: 1.1768 time to fit residues: 310.0880 Evaluate side-chains 246 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 224 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9752 Z= 0.187 Angle : 0.580 10.341 13226 Z= 0.287 Chirality : 0.040 0.135 1525 Planarity : 0.003 0.049 1634 Dihedral : 4.762 34.715 1656 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 21.68 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1190 helix: 2.36 (0.25), residues: 463 sheet: 0.49 (0.29), residues: 305 loop : -0.71 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS A 169 PHE 0.035 0.002 PHE A 430 TYR 0.011 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8731 (mm) cc_final: 0.8516 (mm) REVERT: A 85 GLN cc_start: 0.8141 (tp40) cc_final: 0.7871 (tp-100) REVERT: A 171 ARG cc_start: 0.6844 (mtt-85) cc_final: 0.6335 (mtt-85) REVERT: A 430 PHE cc_start: 0.8231 (m-80) cc_final: 0.7849 (m-80) REVERT: A 443 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: B 261 ASP cc_start: 0.6937 (t70) cc_final: 0.6666 (t0) REVERT: B 295 THR cc_start: 0.8478 (m) cc_final: 0.8118 (p) REVERT: C 258 ASP cc_start: 0.7339 (t70) cc_final: 0.7021 (t0) REVERT: H 5 VAL cc_start: 0.8309 (t) cc_final: 0.8082 (p) outliers start: 25 outliers final: 22 residues processed: 245 average time/residue: 1.2178 time to fit residues: 318.9405 Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098179 restraints weight = 16082.531| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.08 r_work: 0.3321 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9752 Z= 0.184 Angle : 0.585 11.894 13226 Z= 0.290 Chirality : 0.039 0.136 1525 Planarity : 0.003 0.047 1634 Dihedral : 4.775 34.469 1656 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 2.77 % Allowed : 21.39 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1190 helix: 2.40 (0.25), residues: 463 sheet: 0.42 (0.29), residues: 305 loop : -0.67 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS A 169 PHE 0.033 0.002 PHE A 430 TYR 0.012 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4895.88 seconds wall clock time: 87 minutes 20.86 seconds (5240.86 seconds total)