Starting phenix.real_space_refine on Sat Aug 3 09:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/08_2024/7dh5_30678.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/08_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_30678/08_2024/7dh5_30678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/08_2024/7dh5_30678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/08_2024/7dh5_30678.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh5_30678/08_2024/7dh5_30678.cif" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7850 Number of models: 1 Model: "" Number of chains: 6 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: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2052 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259} 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 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'H6U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.55, per 1000 atoms: 0.58 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: 2.81 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 30 helices and 11 sheets defined 41.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 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) removed outlier: 3.742A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.508A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.249A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.957A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.614A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 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 25 removed outlier: 3.693A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.627A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.536A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 Processing helix chain 'R' and resid 72 through 90 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.564A pdb=" N THR R 122 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 241 Processing helix chain 'R' and resid 289 through 318 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 324 through 346 Proline residue: R 343 - end of helix removed outlier: 3.560A pdb=" N TYR R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.236A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (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: 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) Processing sheet with id=AA2, 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=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.866A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.652A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 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=AA7, first strand: chain 'B' and resid 229 through 234 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=AA8, 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) removed outlier: 5.012A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'N' and resid 49 through 50 removed outlier: 3.600A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1119 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: 2.22 Time building geometry restraints manager: 3.09 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: 83 2.58 - 3.16: 6554 3.16 - 3.74: 12116 3.74 - 4.32: 17285 4.32 - 4.90: 29426 Nonbonded interactions: 65464 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.005 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.066 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP R 117 " pdb=" N VAL R 118 " model vdw 2.245 3.120 ... (remaining 65459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.210 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.030 Find NCS groups from input model: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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= 0.550 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 : 0.753 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: 0.2714 time to fit residues: 47.4616 Evaluate side-chains 115 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 88 ASN B 239 ASN B 268 ASN N 1 GLN N 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1366 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= 0.183 Angle : 0.600 6.984 10885 Z= 0.317 Chirality : 0.043 0.193 1258 Planarity : 0.005 0.058 1394 Dihedral : 6.034 74.438 1126 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.72 % Allowed : 12.01 % Favored : 86.27 % 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: -2.07 (0.25), residues: 1011 helix: 0.14 (0.26), residues: 377 sheet: -2.75 (0.31), residues: 203 loop : -1.97 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.035 0.002 PHE R 222 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** 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 145 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.860 Fit side-chains REVERT: A 16 GLU cc_start: 0.7327 (mp0) cc_final: 0.6942 (mp0) REVERT: A 17 LYS cc_start: 0.8375 (tttm) cc_final: 0.8035 (tttt) REVERT: A 209 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6792 (mm-30) REVERT: B 33 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 61 MET cc_start: 0.8594 (ppp) cc_final: 0.8394 (ppp) REVERT: R 238 LEU cc_start: 0.8138 (tt) cc_final: 0.7869 (tp) REVERT: R 242 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8397 (tt) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.2603 time to fit residues: 46.9449 Evaluate side-chains 123 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR 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 115 SER 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: 0.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1710 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= 0.210 Angle : 0.569 7.480 10885 Z= 0.298 Chirality : 0.043 0.219 1258 Planarity : 0.004 0.049 1394 Dihedral : 5.631 71.916 1126 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.06 % Allowed : 14.58 % Favored : 82.35 % 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: -1.42 (0.26), residues: 1011 helix: 0.84 (0.27), residues: 378 sheet: -2.44 (0.31), residues: 205 loop : -1.74 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.006 0.001 HIS A 347 PHE 0.031 0.002 PHE R 222 TYR 0.014 0.001 TYR B 264 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 146 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.814 Fit side-chains REVERT: A 16 GLU cc_start: 0.7308 (mp0) cc_final: 0.6863 (mp0) REVERT: A 17 LYS cc_start: 0.8369 (tttm) cc_final: 0.8031 (tttt) REVERT: A 211 LYS cc_start: 0.8767 (mttp) cc_final: 0.8136 (mtpt) REVERT: A 299 GLU cc_start: 0.7970 (pm20) cc_final: 0.7728 (pm20) REVERT: B 33 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6837 (mp) REVERT: N 108 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8208 (t80) REVERT: R 238 LEU cc_start: 0.8227 (tt) cc_final: 0.7978 (tp) REVERT: R 241 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6924 (mt-10) REVERT: R 242 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 0.2442 time to fit residues: 43.7806 Evaluate side-chains 137 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 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 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 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 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: 7.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1995 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= 0.171 Angle : 0.537 10.290 10885 Z= 0.279 Chirality : 0.042 0.151 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.358 70.053 1126 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.94 % Allowed : 16.42 % Favored : 80.64 % 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: -0.92 (0.26), residues: 1011 helix: 1.34 (0.27), residues: 371 sheet: -2.20 (0.31), residues: 212 loop : -1.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.029 0.002 PHE R 341 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG N 19 *********************** 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 145 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.754 Fit side-chains REVERT: A 16 GLU cc_start: 0.7260 (mp0) cc_final: 0.6780 (mp0) REVERT: A 17 LYS cc_start: 0.8362 (tttm) cc_final: 0.8076 (tttt) REVERT: A 211 LYS cc_start: 0.8620 (mttp) cc_final: 0.8035 (mtpt) REVERT: A 307 ARG cc_start: 0.8034 (ptp-110) cc_final: 0.7646 (mtm-85) REVERT: B 33 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6869 (mp) REVERT: B 234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: N 94 TYR cc_start: 0.8770 (m-80) cc_final: 0.8407 (m-80) REVERT: R 238 LEU cc_start: 0.8234 (tt) cc_final: 0.7987 (tp) REVERT: R 242 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8386 (tt) REVERT: R 357 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7170 (ttp80) outliers start: 24 outliers final: 15 residues processed: 140 average time/residue: 0.2378 time to fit residues: 43.0523 Evaluate side-chains 137 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- 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** A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1942 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= 0.288 Angle : 0.589 10.554 10885 Z= 0.303 Chirality : 0.044 0.162 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.614 69.608 1126 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.04 % Allowed : 17.40 % Favored : 78.55 % 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: -0.72 (0.27), residues: 1011 helix: 1.39 (0.27), residues: 372 sheet: -1.96 (0.31), residues: 224 loop : -1.27 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.008 0.001 HIS A 347 PHE 0.030 0.002 PHE R 222 TYR 0.016 0.001 TYR A 37 ARG 0.005 0.000 ARG N 67 *********************** 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 149 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.888 Fit side-chains REVERT: A 16 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: A 17 LYS cc_start: 0.8339 (tttm) cc_final: 0.8057 (tttt) REVERT: A 211 LYS cc_start: 0.8688 (mttp) cc_final: 0.8121 (mtpt) REVERT: B 33 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6846 (mp) REVERT: B 234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: N 94 TYR cc_start: 0.8801 (m-80) cc_final: 0.8480 (m-80) REVERT: N 108 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8285 (t80) REVERT: R 221 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6495 (mp) REVERT: R 238 LEU cc_start: 0.8229 (tt) cc_final: 0.7965 (tp) REVERT: R 242 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8394 (tt) REVERT: R 357 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7200 (ttp80) outliers start: 33 outliers final: 21 residues processed: 141 average time/residue: 0.2421 time to fit residues: 44.1648 Evaluate side-chains 138 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 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 108 PHE 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 161 VAL Chi-restraints excluded: chain R residue 221 LEU 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: 6.9990 chunk 19 optimal weight: 0.0770 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 75 GLN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8007 Z= 0.146 Angle : 0.538 11.816 10885 Z= 0.277 Chirality : 0.041 0.154 1258 Planarity : 0.004 0.042 1394 Dihedral : 5.255 68.513 1126 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.68 % Allowed : 18.14 % 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: -0.53 (0.27), residues: 1011 helix: 1.64 (0.27), residues: 376 sheet: -1.91 (0.32), residues: 220 loop : -1.27 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.025 0.001 PHE R 222 TYR 0.013 0.001 TYR R 346 ARG 0.004 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 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.839 Fit side-chains REVERT: A 16 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 17 LYS cc_start: 0.8348 (tttm) cc_final: 0.8076 (tttt) REVERT: A 211 LYS cc_start: 0.8593 (mttp) cc_final: 0.8076 (mtpt) REVERT: B 33 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 153 ASP cc_start: 0.8211 (m-30) cc_final: 0.7874 (m-30) REVERT: B 217 MET cc_start: 0.7466 (ppp) cc_final: 0.6811 (ppp) REVERT: B 234 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: N 94 TYR cc_start: 0.8735 (m-80) cc_final: 0.8530 (m-80) REVERT: R 148 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7766 (tt) REVERT: R 238 LEU cc_start: 0.8193 (tt) cc_final: 0.7934 (tp) REVERT: R 242 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8399 (tt) REVERT: R 357 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7182 (ttp80) outliers start: 30 outliers final: 14 residues processed: 142 average time/residue: 0.2384 time to fit residues: 43.9296 Evaluate side-chains 131 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 299 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE 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 107 CYS Chi-restraints excluded: chain N residue 126 VAL 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 161 VAL 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: 5.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8007 Z= 0.256 Angle : 0.564 11.713 10885 Z= 0.292 Chirality : 0.043 0.178 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.469 68.455 1126 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.55 % Allowed : 18.50 % Favored : 77.94 % 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: -0.39 (0.27), residues: 1011 helix: 1.72 (0.27), residues: 371 sheet: -1.87 (0.32), residues: 221 loop : -1.09 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.027 0.002 PHE R 222 TYR 0.015 0.002 TYR A 37 ARG 0.004 0.000 ARG B 256 *********************** 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 147 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.889 Fit side-chains REVERT: A 16 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: A 17 LYS cc_start: 0.8328 (tttm) cc_final: 0.8058 (tttt) REVERT: A 211 LYS cc_start: 0.8621 (mttp) cc_final: 0.8126 (mtpp) REVERT: A 307 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7747 (mtm-85) REVERT: B 33 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6911 (mp) REVERT: B 153 ASP cc_start: 0.8176 (m-30) cc_final: 0.7940 (m-30) REVERT: B 234 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: N 94 TYR cc_start: 0.8770 (m-80) cc_final: 0.8561 (m-80) REVERT: N 98 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8057 (ppt170) REVERT: R 148 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7801 (tt) REVERT: R 238 LEU cc_start: 0.8234 (tt) cc_final: 0.7962 (tp) REVERT: R 242 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8403 (tt) REVERT: R 357 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7224 (ttp80) outliers start: 29 outliers final: 20 residues processed: 140 average time/residue: 0.2430 time to fit residues: 43.9766 Evaluate side-chains 139 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG 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 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 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: 1.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8007 Z= 0.219 Angle : 0.554 12.262 10885 Z= 0.285 Chirality : 0.042 0.183 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.384 68.231 1126 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.17 % Allowed : 18.50 % Favored : 77.33 % 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: -0.27 (0.27), residues: 1011 helix: 1.81 (0.27), residues: 371 sheet: -1.81 (0.32), residues: 218 loop : -1.03 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.025 0.002 PHE R 222 TYR 0.015 0.001 TYR R 346 ARG 0.003 0.000 ARG N 19 *********************** 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 150 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 0.804 Fit side-chains REVERT: A 16 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 17 LYS cc_start: 0.8300 (tttm) cc_final: 0.8027 (tttt) REVERT: A 211 LYS cc_start: 0.8566 (mttp) cc_final: 0.8104 (mtpp) REVERT: A 307 ARG cc_start: 0.8069 (ptp-110) cc_final: 0.7705 (mtm-85) REVERT: B 33 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6896 (mp) REVERT: B 153 ASP cc_start: 0.8129 (m-30) cc_final: 0.7914 (m-30) REVERT: B 217 MET cc_start: 0.7505 (ppp) cc_final: 0.6822 (ppp) REVERT: B 234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: N 98 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7986 (ppt170) REVERT: R 148 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7813 (tt) REVERT: R 238 LEU cc_start: 0.8218 (tt) cc_final: 0.7943 (tp) REVERT: R 242 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8380 (tt) REVERT: R 357 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7186 (ttp80) outliers start: 34 outliers final: 24 residues processed: 141 average time/residue: 0.2417 time to fit residues: 43.8502 Evaluate side-chains 147 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN 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 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG 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 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 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8007 Z= 0.145 Angle : 0.522 14.124 10885 Z= 0.266 Chirality : 0.041 0.183 1258 Planarity : 0.004 0.040 1394 Dihedral : 5.022 66.222 1126 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.55 % Allowed : 19.24 % Favored : 77.21 % 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: -0.17 (0.27), residues: 1011 helix: 2.00 (0.27), residues: 376 sheet: -1.84 (0.31), residues: 228 loop : -1.03 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.023 0.001 PHE R 222 TYR 0.011 0.001 TYR R 346 ARG 0.003 0.000 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 151 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.820 Fit side-chains REVERT: A 307 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7651 (mtm-85) REVERT: B 33 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6787 (mp) REVERT: B 234 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: N 98 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7814 (ppt170) REVERT: R 64 ARG cc_start: 0.7449 (ptp-170) cc_final: 0.7193 (ptp-110) REVERT: R 238 LEU cc_start: 0.8199 (tt) cc_final: 0.7926 (tp) REVERT: R 357 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7152 (ttp80) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.2576 time to fit residues: 46.7774 Evaluate side-chains 140 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 98 ARG 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 89 LEU Chi-restraints excluded: chain R residue 115 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7517 > 50: distance: 31 - 91: 34.348 distance: 34 - 88: 32.800 distance: 44 - 51: 27.306 distance: 51 - 52: 45.594 distance: 52 - 53: 55.278 distance: 53 - 56: 40.287 distance: 56 - 57: 56.954 distance: 56 - 62: 39.109 distance: 57 - 58: 57.792 distance: 58 - 59: 39.954 distance: 58 - 63: 39.274 distance: 60 - 61: 44.258 distance: 61 - 62: 19.777 distance: 63 - 64: 14.548 distance: 64 - 65: 16.785 distance: 65 - 66: 41.621 distance: 65 - 67: 37.198 distance: 68 - 69: 52.768 distance: 69 - 76: 51.502 distance: 71 - 72: 56.063 distance: 72 - 73: 55.065 distance: 73 - 74: 57.466 distance: 74 - 75: 39.192 distance: 76 - 77: 39.559 distance: 78 - 79: 69.833 distance: 78 - 80: 55.315 distance: 80 - 81: 57.037 distance: 81 - 82: 38.741 distance: 81 - 84: 40.264 distance: 82 - 83: 69.506 distance: 84 - 85: 40.354 distance: 85 - 86: 39.832 distance: 85 - 87: 56.880 distance: 89 - 92: 56.354 distance: 93 - 94: 40.016 distance: 94 - 95: 39.656 distance: 97 - 98: 56.865 distance: 99 - 100: 56.846 distance: 103 - 105: 40.167 distance: 104 - 106: 40.944 distance: 104 - 107: 55.636 distance: 107 - 109: 55.356 distance: 109 - 110: 40.863 distance: 111 - 112: 37.645 distance: 112 - 113: 67.253 distance: 112 - 115: 54.628 distance: 113 - 114: 55.917 distance: 113 - 118: 41.242 distance: 115 - 116: 57.641 distance: 115 - 117: 55.969 distance: 119 - 120: 50.223 distance: 119 - 122: 20.230 distance: 120 - 121: 9.278 distance: 120 - 124: 31.329 distance: 122 - 123: 46.273