Starting phenix.real_space_refine on Mon Mar 11 09:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/03_2024/7dh5_30678_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 47 5.16 5 C 4975 2.51 5 N 1383 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "R PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 236": "NH1" <-> "NH2" Residue "R ARG 239": "NH1" <-> "NH2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R GLU 241": "OE1" <-> "OE2" Residue "R ARG 289": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 353": "NH1" <-> "NH2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ARG 358": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7850 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2080 Unusual residues: {'H6U': 1} Classifications: {'peptide': 276, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259, None: 1} Not linked: pdbres="LEU R 360 " pdbres="H6U R 401 " Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.40, per 1000 atoms: 0.56 Number of scatterers: 7850 At special positions: 0 Unit cell: (98.5625, 79.8875, 132.8, 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 47 16.00 O 1445 8.00 N 1383 7.00 C 4975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 36.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.649A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.614A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 removed outlier: 3.638A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.043A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.110A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 38 through 63 removed outlier: 4.140A pdb=" N ALA R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 Processing helix chain 'R' and resid 91 through 99 Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.564A pdb=" N THR R 122 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 169 Processing helix chain 'R' and resid 189 through 191 No H-bonds generated for 'chain 'R' and resid 189 through 191' Processing helix chain 'R' and resid 202 through 212 Processing helix chain 'R' and resid 214 through 240 Processing helix chain 'R' and resid 290 through 317 removed outlier: 4.314A pdb=" N CYS R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 325 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 350 through 357 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.497A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.667A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.951A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.641A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.659A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.414A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.648A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.601A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1017 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: 2.14 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1277 1.31 - 1.44: 2179 1.44 - 1.56: 4488 1.56 - 1.69: 2 1.69 - 1.81: 61 Bond restraints: 8007 Sorted by residual: bond pdb=" C27 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.731 1.589 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.742 1.616 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C06 H6U R 401 " pdb=" N08 H6U R 401 " ideal model delta sigma weight residual 1.353 1.464 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.333 1.209 0.124 2.74e-02 1.33e+03 2.03e+01 bond pdb=" C02 H6U R 401 " pdb=" N01 H6U R 401 " ideal model delta sigma weight residual 1.348 1.438 -0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 8002 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.97: 149 105.97 - 113.01: 4374 113.01 - 120.05: 2841 120.05 - 127.09: 3429 127.09 - 134.12: 92 Bond angle restraints: 10885 Sorted by residual: angle pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" C ILE A 365 " ideal model delta sigma weight residual 112.35 106.61 5.74 1.41e+00 5.03e-01 1.66e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.31 114.26 6.05 1.52e+00 4.33e-01 1.58e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.16 107.84 5.32 1.49e+00 4.50e-01 1.27e+01 angle pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " pdb=" C27 H6U R 401 " ideal model delta sigma weight residual 89.03 98.94 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.15 110.75 11.40 3.47e+00 8.31e-02 1.08e+01 ... (remaining 10880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4310 18.01 - 36.03: 376 36.03 - 54.04: 59 54.04 - 72.06: 14 72.06 - 90.07: 5 Dihedral angle restraints: 4764 sinusoidal: 1788 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 158.35 -65.35 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -146.23 -33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -122.50 36.50 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 708 0.036 - 0.072: 386 0.072 - 0.109: 124 0.109 - 0.145: 37 0.145 - 0.181: 3 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CA PHE R 222 " pdb=" N PHE R 222 " pdb=" C PHE R 222 " pdb=" CB PHE R 222 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 108 " -0.023 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE N 108 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE N 108 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE N 108 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE N 108 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE N 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE N 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 308 " -0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE R 308 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 308 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 308 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE R 308 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 308 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 322 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.024 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 87 2.58 - 3.16: 6576 3.16 - 3.74: 12166 3.74 - 4.32: 17381 4.32 - 4.90: 29442 Nonbonded interactions: 65652 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.005 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.066 2.440 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASP R 117 " pdb=" N VAL R 118 " model vdw 2.245 2.520 ... (remaining 65647 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: 0.200 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: 1.190 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 24.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.008 0.142 8007 Z= 0.568 Angle : 0.798 11.404 10885 Z= 0.442 Chirality : 0.049 0.181 1258 Planarity : 0.005 0.044 1394 Dihedral : 14.096 90.073 2826 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1011 helix: -1.82 (0.22), residues: 378 sheet: -3.37 (0.28), residues: 201 loop : -2.54 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 99 HIS 0.012 0.002 HIS A 347 PHE 0.061 0.003 PHE N 108 TYR 0.017 0.002 TYR B 59 ARG 0.012 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8301 (tttm) cc_final: 0.7973 (tttt) REVERT: A 323 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6752 (mtm180) REVERT: B 61 MET cc_start: 0.8785 (ppp) cc_final: 0.8464 (ppp) REVERT: B 111 TYR cc_start: 0.8725 (m-80) cc_final: 0.8494 (m-80) REVERT: B 219 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7147 (mtp-110) REVERT: R 238 LEU cc_start: 0.8186 (tt) cc_final: 0.7864 (tp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2894 time to fit residues: 50.7580 Evaluate side-chains 115 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 213 GLN A 261 ASN A 268 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN N 1 GLN N 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8007 Z= 0.182 Angle : 0.568 7.415 10885 Z= 0.295 Chirality : 0.043 0.185 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.983 74.443 1126 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.84 % Allowed : 12.99 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.25), residues: 1011 helix: 0.01 (0.25), residues: 373 sheet: -2.86 (0.30), residues: 204 loop : -1.79 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.035 0.002 PHE R 222 TYR 0.010 0.001 TYR A 329 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.883 Fit side-chains REVERT: A 17 LYS cc_start: 0.8363 (tttm) cc_final: 0.8038 (tttt) REVERT: A 209 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6589 (mm-30) REVERT: B 33 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6951 (mp) REVERT: B 61 MET cc_start: 0.8597 (ppp) cc_final: 0.8365 (ppp) REVERT: B 156 GLN cc_start: 0.7876 (tt0) cc_final: 0.7643 (tt0) REVERT: B 219 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.7225 (mtp-110) REVERT: R 238 LEU cc_start: 0.8190 (tt) cc_final: 0.7932 (tp) REVERT: R 242 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8428 (tt) outliers start: 15 outliers final: 7 residues processed: 146 average time/residue: 0.2672 time to fit residues: 50.1037 Evaluate side-chains 126 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.0000 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8007 Z= 0.245 Angle : 0.569 9.116 10885 Z= 0.293 Chirality : 0.043 0.208 1258 Planarity : 0.004 0.064 1394 Dihedral : 5.696 72.402 1126 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.92 % Allowed : 14.71 % Favored : 81.37 % 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: -1.53 (0.25), residues: 1011 helix: 0.57 (0.26), residues: 375 sheet: -2.52 (0.30), residues: 206 loop : -1.58 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.032 0.002 PHE R 222 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.871 Fit side-chains REVERT: A 16 GLU cc_start: 0.7300 (mp0) cc_final: 0.6854 (mp0) REVERT: A 17 LYS cc_start: 0.8352 (tttm) cc_final: 0.8031 (tttt) REVERT: A 209 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 211 LYS cc_start: 0.8818 (mttp) cc_final: 0.8167 (mtpt) REVERT: A 299 GLU cc_start: 0.7995 (pm20) cc_final: 0.7624 (pm20) REVERT: B 33 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.6961 (mp) REVERT: B 35 ASN cc_start: 0.7479 (m-40) cc_final: 0.7190 (m-40) REVERT: B 156 GLN cc_start: 0.8000 (tt0) cc_final: 0.7789 (tt0) REVERT: B 219 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7272 (mtp-110) REVERT: N 94 TYR cc_start: 0.8850 (m-80) cc_final: 0.8427 (m-80) REVERT: R 238 LEU cc_start: 0.8274 (tt) cc_final: 0.7974 (tp) REVERT: R 242 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8415 (tt) outliers start: 32 outliers final: 25 residues processed: 143 average time/residue: 0.2442 time to fit residues: 44.8770 Evaluate side-chains 147 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 81 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8007 Z= 0.256 Angle : 0.559 7.794 10885 Z= 0.288 Chirality : 0.043 0.154 1258 Planarity : 0.004 0.064 1394 Dihedral : 5.604 70.980 1126 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.17 % Allowed : 16.05 % Favored : 79.78 % 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 (0.26), residues: 1011 helix: 0.95 (0.26), residues: 369 sheet: -2.15 (0.30), residues: 225 loop : -1.32 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.030 0.002 PHE R 222 TYR 0.014 0.001 TYR A 37 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.880 Fit side-chains REVERT: A 16 GLU cc_start: 0.7288 (mp0) cc_final: 0.6815 (mp0) REVERT: A 17 LYS cc_start: 0.8365 (tttm) cc_final: 0.8050 (tttt) REVERT: A 209 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6578 (mm-30) REVERT: A 211 LYS cc_start: 0.8789 (mttp) cc_final: 0.8149 (mtpt) REVERT: A 299 GLU cc_start: 0.8012 (pm20) cc_final: 0.7747 (pm20) REVERT: A 307 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7722 (mtm-85) REVERT: B 33 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.6966 (mp) REVERT: B 35 ASN cc_start: 0.7570 (m-40) cc_final: 0.7319 (m-40) REVERT: N 94 TYR cc_start: 0.8852 (m-80) cc_final: 0.8554 (m-80) REVERT: N 108 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8259 (t80) REVERT: R 238 LEU cc_start: 0.8303 (tt) cc_final: 0.8042 (tp) REVERT: R 242 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 34 outliers final: 27 residues processed: 145 average time/residue: 0.2339 time to fit residues: 44.1702 Evaluate side-chains 147 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8007 Z= 0.159 Angle : 0.512 6.699 10885 Z= 0.264 Chirality : 0.041 0.157 1258 Planarity : 0.004 0.063 1394 Dihedral : 5.266 69.672 1126 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.19 % Allowed : 18.63 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1011 helix: 1.23 (0.26), residues: 374 sheet: -2.02 (0.30), residues: 219 loop : -1.21 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 PHE 0.028 0.002 PHE R 341 TYR 0.012 0.001 TYR R 346 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.976 Fit side-chains REVERT: A 16 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 17 LYS cc_start: 0.8384 (tttm) cc_final: 0.8101 (tttt) REVERT: A 211 LYS cc_start: 0.8703 (mttp) cc_final: 0.8102 (mtpt) REVERT: A 307 ARG cc_start: 0.8045 (ptp-110) cc_final: 0.7659 (mtm-85) REVERT: A 361 ASN cc_start: 0.8656 (t0) cc_final: 0.8428 (m-40) REVERT: B 33 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6860 (mp) REVERT: B 35 ASN cc_start: 0.7623 (m-40) cc_final: 0.7382 (m-40) REVERT: N 94 TYR cc_start: 0.8759 (m-80) cc_final: 0.8540 (m-80) REVERT: R 238 LEU cc_start: 0.8264 (tt) cc_final: 0.8026 (tp) REVERT: R 242 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8470 (tt) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.2439 time to fit residues: 46.0336 Evaluate side-chains 142 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 0.0040 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8007 Z= 0.284 Angle : 0.561 6.851 10885 Z= 0.290 Chirality : 0.043 0.179 1258 Planarity : 0.004 0.066 1394 Dihedral : 5.543 69.565 1126 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.53 % Allowed : 19.12 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 1011 helix: 1.35 (0.26), residues: 368 sheet: -1.94 (0.30), residues: 222 loop : -1.09 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.008 0.001 HIS A 347 PHE 0.030 0.002 PHE R 341 TYR 0.016 0.002 TYR R 346 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 0.917 Fit side-chains REVERT: A 17 LYS cc_start: 0.8332 (tttm) cc_final: 0.8055 (tttt) REVERT: A 211 LYS cc_start: 0.8678 (mttp) cc_final: 0.8102 (mtpt) REVERT: B 33 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.6888 (mp) REVERT: R 148 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7729 (tt) REVERT: R 238 LEU cc_start: 0.8325 (tt) cc_final: 0.7993 (tp) REVERT: R 242 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8499 (tt) outliers start: 37 outliers final: 28 residues processed: 145 average time/residue: 0.2379 time to fit residues: 44.9631 Evaluate side-chains 146 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8007 Z= 0.147 Angle : 0.499 6.769 10885 Z= 0.257 Chirality : 0.041 0.170 1258 Planarity : 0.004 0.070 1394 Dihedral : 5.117 68.822 1126 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.92 % Allowed : 19.85 % Favored : 76.23 % 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: -0.33 (0.26), residues: 1011 helix: 1.69 (0.26), residues: 372 sheet: -1.67 (0.31), residues: 215 loop : -1.10 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 PHE 0.031 0.001 PHE R 341 TYR 0.013 0.001 TYR R 346 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 0.873 Fit side-chains REVERT: A 16 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 17 LYS cc_start: 0.8337 (tttm) cc_final: 0.8100 (tttt) REVERT: A 211 LYS cc_start: 0.8564 (mttp) cc_final: 0.8045 (mtpt) REVERT: A 286 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 307 ARG cc_start: 0.7958 (ptp-110) cc_final: 0.7647 (mtm-85) REVERT: A 361 ASN cc_start: 0.8647 (t0) cc_final: 0.8422 (m-40) REVERT: B 33 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.6846 (mp) REVERT: R 148 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7763 (tt) REVERT: R 238 LEU cc_start: 0.8237 (tt) cc_final: 0.7991 (tp) REVERT: R 242 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8477 (tt) REVERT: R 357 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7108 (ttp80) outliers start: 32 outliers final: 22 residues processed: 148 average time/residue: 0.2297 time to fit residues: 44.3346 Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8007 Z= 0.215 Angle : 0.526 8.136 10885 Z= 0.270 Chirality : 0.042 0.185 1258 Planarity : 0.004 0.071 1394 Dihedral : 5.262 68.236 1126 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.53 % Allowed : 19.73 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1011 helix: 1.77 (0.26), residues: 369 sheet: -1.71 (0.31), residues: 221 loop : -0.98 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS A 347 PHE 0.032 0.002 PHE R 341 TYR 0.014 0.001 TYR A 37 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 0.889 Fit side-chains REVERT: A 16 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 17 LYS cc_start: 0.8349 (tttm) cc_final: 0.8104 (tttt) REVERT: A 211 LYS cc_start: 0.8613 (mttp) cc_final: 0.8104 (mtpp) REVERT: A 286 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 361 ASN cc_start: 0.8700 (t0) cc_final: 0.8447 (m-40) REVERT: B 33 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 152 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (tt) REVERT: R 148 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7779 (tt) REVERT: R 238 LEU cc_start: 0.8264 (tt) cc_final: 0.8002 (tp) REVERT: R 242 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8468 (tt) REVERT: R 357 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7160 (ttp80) outliers start: 37 outliers final: 27 residues processed: 148 average time/residue: 0.2342 time to fit residues: 45.1500 Evaluate side-chains 152 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8007 Z= 0.429 Angle : 0.633 8.904 10885 Z= 0.326 Chirality : 0.046 0.218 1258 Planarity : 0.005 0.073 1394 Dihedral : 5.819 70.257 1126 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.66 % Allowed : 19.73 % Favored : 75.61 % 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: -0.63 (0.26), residues: 1011 helix: 1.23 (0.26), residues: 381 sheet: -1.78 (0.31), residues: 220 loop : -1.12 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.009 0.002 HIS A 347 PHE 0.031 0.003 PHE R 222 TYR 0.020 0.002 TYR A 37 ARG 0.007 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 0.905 Fit side-chains REVERT: A 17 LYS cc_start: 0.8335 (tttm) cc_final: 0.8069 (tttt) REVERT: A 211 LYS cc_start: 0.8711 (mttp) cc_final: 0.8175 (mtpt) REVERT: A 307 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7732 (mtm-85) REVERT: B 33 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6947 (mp) REVERT: B 152 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (tt) REVERT: R 148 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7732 (tt) REVERT: R 238 LEU cc_start: 0.8440 (tt) cc_final: 0.8106 (tp) REVERT: R 242 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8377 (tt) REVERT: R 357 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7246 (ttp80) outliers start: 38 outliers final: 27 residues processed: 145 average time/residue: 0.2408 time to fit residues: 45.3611 Evaluate side-chains 144 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.204 Angle : 0.548 8.860 10885 Z= 0.280 Chirality : 0.042 0.194 1258 Planarity : 0.004 0.077 1394 Dihedral : 5.425 70.447 1126 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.31 % Allowed : 20.96 % Favored : 75.74 % 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: -0.41 (0.26), residues: 1011 helix: 1.59 (0.26), residues: 374 sheet: -1.76 (0.31), residues: 219 loop : -1.08 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.005 0.001 HIS A 347 PHE 0.033 0.002 PHE R 341 TYR 0.013 0.001 TYR N 80 ARG 0.006 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.880 Fit side-chains REVERT: A 17 LYS cc_start: 0.8332 (tttm) cc_final: 0.8065 (tttt) REVERT: A 211 LYS cc_start: 0.8577 (mttp) cc_final: 0.8104 (mtpp) REVERT: A 307 ARG cc_start: 0.7977 (ptp-110) cc_final: 0.7713 (mtm-85) REVERT: A 361 ASN cc_start: 0.8727 (t0) cc_final: 0.8466 (t0) REVERT: B 33 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6871 (mp) REVERT: R 148 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7701 (tt) REVERT: R 238 LEU cc_start: 0.8283 (tt) cc_final: 0.8014 (tp) REVERT: R 242 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8426 (tt) REVERT: R 357 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7167 (ttp80) outliers start: 27 outliers final: 23 residues processed: 142 average time/residue: 0.2373 time to fit residues: 44.0619 Evaluate side-chains 145 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115473 restraints weight = 8400.053| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.57 r_work: 0.3158 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8007 Z= 0.132 Angle : 0.511 8.389 10885 Z= 0.260 Chirality : 0.041 0.190 1258 Planarity : 0.004 0.078 1394 Dihedral : 4.988 68.788 1126 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.82 % Allowed : 21.57 % Favored : 75.61 % 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: -0.16 (0.26), residues: 1011 helix: 1.81 (0.26), residues: 378 sheet: -1.64 (0.31), residues: 220 loop : -0.97 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.003 0.001 HIS A 347 PHE 0.033 0.001 PHE R 341 TYR 0.011 0.001 TYR N 80 ARG 0.006 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.77 seconds wall clock time: 35 minutes 43.69 seconds (2143.69 seconds total)