Starting phenix.real_space_refine on Thu Jan 18 12:28:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/01_2024/7l1u_23118_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.026 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 63 5.16 5 C 5586 2.51 5 N 1498 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 337": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2496 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 422 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1719 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2220 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 64 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 8} Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8723 At special positions: 0 Unit cell: (112.56, 108.36, 137.76, 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 63 16.00 O 1576 8.00 N 1498 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 32.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.752A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.184A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 6 through 22 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'R' and resid 53 through 55 No H-bonds generated for 'chain 'R' and resid 53 through 55' Processing helix chain 'R' and resid 57 through 81 Processing helix chain 'R' and resid 90 through 106 Processing helix chain 'R' and resid 108 through 117 Processing helix chain 'R' and resid 123 through 156 Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 166 through 189 removed outlier: 3.854A pdb=" N MET R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE R 185 " --> pdb=" O CYS R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 219 through 231 Processing helix chain 'R' and resid 233 through 249 Processing helix chain 'R' and resid 293 through 315 removed outlier: 4.153A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 327 Processing helix chain 'R' and resid 339 through 363 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 375 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.318A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 218 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.017A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.936A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.177A 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: 6.678A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.614A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 335 through 339 removed outlier: 3.762A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.523A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.545A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 226 through 231 removed outlier: 6.346A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 191 through 195 391 hydrogen bonds defined for protein. 1128 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: 2.53 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2678 1.34 - 1.46: 1900 1.46 - 1.58: 4241 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8911 Sorted by residual: bond pdb=" C MET L 28 " pdb=" N NH2 L 29 " ideal model delta sigma weight residual 2.329 1.225 1.104 1.40e-02 5.10e+03 6.22e+03 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.722 0.086 3.30e-02 9.18e+02 6.85e+00 bond pdb=" CA GLN H 142 " pdb=" CB GLN H 142 " ideal model delta sigma weight residual 1.527 1.462 0.065 2.48e-02 1.63e+03 6.83e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.52e+00 bond pdb=" C TYR A 360 " pdb=" N PRO A 361 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.11e-02 8.12e+03 6.03e+00 ... (remaining 8906 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.33: 144 105.33 - 112.53: 4598 112.53 - 119.73: 3091 119.73 - 126.93: 4170 126.93 - 134.13: 113 Bond angle restraints: 12116 Sorted by residual: angle pdb=" C LYS B 301 " pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C PRO B 236 " pdb=" N ASN B 237 " pdb=" CA ASN B 237 " ideal model delta sigma weight residual 122.38 115.79 6.59 1.81e+00 3.05e-01 1.32e+01 angle pdb=" C VAL H 48 " pdb=" N ALA H 49 " pdb=" CA ALA H 49 " ideal model delta sigma weight residual 121.75 115.93 5.82 1.73e+00 3.34e-01 1.13e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 116.01 110.71 5.30 1.64e+00 3.72e-01 1.04e+01 ... (remaining 12111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 4637 15.93 - 31.85: 498 31.85 - 47.78: 93 47.78 - 63.71: 14 63.71 - 79.64: 4 Dihedral angle restraints: 5246 sinusoidal: 1905 harmonic: 3341 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER H 208 " pdb=" C SER H 208 " pdb=" N GLY H 209 " pdb=" CA GLY H 209 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALA R 234 " pdb=" C ALA R 234 " pdb=" N PRO R 235 " pdb=" CA PRO R 235 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 878 0.050 - 0.100: 391 0.100 - 0.150: 113 0.150 - 0.200: 19 0.200 - 0.250: 8 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CB VAL R 73 " pdb=" CA VAL R 73 " pdb=" CG1 VAL R 73 " pdb=" CG2 VAL R 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1406 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 234 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO R 235 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 236 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO B 194 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.038 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1122 2.74 - 3.28: 7707 3.28 - 3.82: 13864 3.82 - 4.36: 16030 4.36 - 4.90: 29405 Nonbonded interactions: 68128 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.202 2.440 nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.288 2.440 nonbonded pdb=" O VAL R 114 " pdb=" OH TYR R 343 " model vdw 2.307 2.440 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.308 2.440 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.315 2.440 ... (remaining 68123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 6.010 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.910 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.016 1.104 8911 Z= 1.157 Angle : 0.998 10.490 12116 Z= 0.571 Chirality : 0.062 0.250 1409 Planarity : 0.007 0.075 1519 Dihedral : 13.515 79.637 3077 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.78 % Allowed : 9.22 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.21 (0.20), residues: 1128 helix: -2.10 (0.20), residues: 391 sheet: -1.25 (0.28), residues: 294 loop : -2.62 (0.23), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 47 HIS 0.008 0.002 HIS B 142 PHE 0.031 0.003 PHE B 199 TYR 0.037 0.003 TYR B 59 ARG 0.007 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.954 Fit side-chains REVERT: A 209 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 293 ASN cc_start: 0.8425 (p0) cc_final: 0.8137 (p0) REVERT: C 47 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7554 (mp0) REVERT: H 87 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: R 122 PHE cc_start: 0.6672 (m-80) cc_final: 0.6379 (m-80) REVERT: R 191 MET cc_start: 0.8699 (mmt) cc_final: 0.8118 (mmp) REVERT: R 239 MET cc_start: 0.8077 (ttm) cc_final: 0.7823 (mtp) REVERT: R 339 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.6497 (ttt-90) outliers start: 7 outliers final: 5 residues processed: 155 average time/residue: 0.2596 time to fit residues: 52.6857 Evaluate side-chains 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 88 ASN H 142 GLN H 171 ASN R 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8911 Z= 0.132 Angle : 0.505 5.742 12116 Z= 0.272 Chirality : 0.041 0.154 1409 Planarity : 0.004 0.053 1519 Dihedral : 4.839 37.415 1246 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.56 % Allowed : 14.56 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.41 (0.23), residues: 1128 helix: 0.15 (0.26), residues: 387 sheet: -0.44 (0.30), residues: 261 loop : -2.13 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.006 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.957 Fit side-chains REVERT: A 209 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8010 (mt-10) REVERT: A 211 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (mtmm) REVERT: B 76 ASP cc_start: 0.8792 (p0) cc_final: 0.8484 (p0) REVERT: B 130 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 293 ASN cc_start: 0.8202 (p0) cc_final: 0.7956 (p0) REVERT: C 47 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7559 (mp0) REVERT: H 71 SER cc_start: 0.7372 (t) cc_final: 0.7110 (p) REVERT: R 122 PHE cc_start: 0.6671 (m-80) cc_final: 0.6460 (m-80) REVERT: R 183 ILE cc_start: 0.8651 (tp) cc_final: 0.8410 (tt) REVERT: R 191 MET cc_start: 0.8783 (mmt) cc_final: 0.8563 (mmp) REVERT: R 339 ARG cc_start: 0.7177 (ptm-80) cc_final: 0.6739 (ttt180) outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.2117 time to fit residues: 44.0005 Evaluate side-chains 138 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 100 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8911 Z= 0.242 Angle : 0.528 5.809 12116 Z= 0.284 Chirality : 0.043 0.150 1409 Planarity : 0.004 0.048 1519 Dihedral : 4.686 37.798 1245 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.56 % Allowed : 17.11 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1128 helix: 1.01 (0.27), residues: 392 sheet: -0.38 (0.30), residues: 267 loop : -1.81 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.016 0.001 PHE B 199 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.055 Fit side-chains REVERT: B 130 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 293 ASN cc_start: 0.8262 (p0) cc_final: 0.7954 (p0) REVERT: C 47 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7546 (mp0) REVERT: H 13 GLN cc_start: 0.8405 (mm110) cc_final: 0.8182 (mm-40) REVERT: H 71 SER cc_start: 0.7503 (t) cc_final: 0.7174 (p) REVERT: R 122 PHE cc_start: 0.6681 (m-80) cc_final: 0.6423 (m-80) REVERT: R 191 MET cc_start: 0.8820 (mmt) cc_final: 0.8541 (mmp) REVERT: R 339 ARG cc_start: 0.7194 (ptm-80) cc_final: 0.6699 (ttt180) outliers start: 23 outliers final: 20 residues processed: 140 average time/residue: 0.2248 time to fit residues: 43.0383 Evaluate side-chains 142 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8911 Z= 0.446 Angle : 0.618 5.897 12116 Z= 0.334 Chirality : 0.046 0.190 1409 Planarity : 0.004 0.046 1519 Dihedral : 5.134 39.610 1245 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.89 % Allowed : 17.89 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.68 (0.25), residues: 1128 helix: 1.15 (0.27), residues: 393 sheet: -0.81 (0.29), residues: 271 loop : -1.62 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.005 0.001 HIS A 362 PHE 0.022 0.002 PHE B 199 TYR 0.018 0.002 TYR H 190 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.029 Fit side-chains REVERT: A 209 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 130 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 273 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 293 ASN cc_start: 0.8385 (p0) cc_final: 0.8074 (p0) REVERT: C 47 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7501 (mp0) REVERT: H 71 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7225 (p) REVERT: R 122 PHE cc_start: 0.6823 (m-80) cc_final: 0.6513 (m-80) REVERT: R 191 MET cc_start: 0.8771 (mmt) cc_final: 0.8501 (mmp) outliers start: 35 outliers final: 27 residues processed: 146 average time/residue: 0.1986 time to fit residues: 40.8687 Evaluate side-chains 148 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8911 Z= 0.215 Angle : 0.514 7.016 12116 Z= 0.274 Chirality : 0.042 0.145 1409 Planarity : 0.003 0.040 1519 Dihedral : 4.646 37.881 1245 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.11 % Allowed : 19.56 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.30 (0.25), residues: 1128 helix: 1.52 (0.27), residues: 391 sheet: -0.52 (0.31), residues: 258 loop : -1.47 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR H 190 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 0.983 Fit side-chains REVERT: B 130 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 293 ASN cc_start: 0.8328 (p0) cc_final: 0.8041 (p0) REVERT: C 47 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7535 (mp0) REVERT: H 71 SER cc_start: 0.7509 (t) cc_final: 0.7141 (p) REVERT: R 122 PHE cc_start: 0.6745 (m-80) cc_final: 0.6442 (m-80) REVERT: R 165 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7801 (p) REVERT: R 191 MET cc_start: 0.8767 (mmt) cc_final: 0.8468 (mmp) outliers start: 28 outliers final: 24 residues processed: 144 average time/residue: 0.1969 time to fit residues: 40.3035 Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8911 Z= 0.201 Angle : 0.504 7.190 12116 Z= 0.267 Chirality : 0.042 0.144 1409 Planarity : 0.003 0.040 1519 Dihedral : 4.466 37.153 1245 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.78 % Allowed : 19.56 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.11 (0.25), residues: 1128 helix: 1.69 (0.28), residues: 391 sheet: -0.45 (0.31), residues: 256 loop : -1.34 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR H 190 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.058 Fit side-chains REVERT: A 280 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7895 (ptm-80) REVERT: B 59 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: B 293 ASN cc_start: 0.8281 (p0) cc_final: 0.8059 (p0) REVERT: C 47 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7510 (mp0) REVERT: H 71 SER cc_start: 0.7545 (OUTLIER) cc_final: 0.7170 (p) REVERT: R 122 PHE cc_start: 0.6730 (m-80) cc_final: 0.6432 (m-80) REVERT: R 165 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7735 (p) REVERT: R 184 MET cc_start: 0.8212 (mmt) cc_final: 0.7310 (mtp) REVERT: R 191 MET cc_start: 0.8743 (mmt) cc_final: 0.8467 (mmp) outliers start: 34 outliers final: 27 residues processed: 151 average time/residue: 0.1916 time to fit residues: 40.5188 Evaluate side-chains 154 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN R 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8911 Z= 0.144 Angle : 0.476 6.117 12116 Z= 0.251 Chirality : 0.041 0.141 1409 Planarity : 0.003 0.039 1519 Dihedral : 4.196 36.742 1245 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.67 % Allowed : 19.78 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.11 (0.25), residues: 1128 helix: 1.85 (0.28), residues: 392 sheet: -0.29 (0.31), residues: 254 loop : -1.22 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR H 190 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 0.991 Fit side-chains REVERT: B 59 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: C 47 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7505 (mp0) REVERT: H 71 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7158 (p) REVERT: R 98 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7345 (mp) REVERT: R 122 PHE cc_start: 0.6711 (m-80) cc_final: 0.6417 (m-80) REVERT: R 151 ASP cc_start: 0.8147 (t70) cc_final: 0.7423 (t0) REVERT: R 191 MET cc_start: 0.8720 (mmt) cc_final: 0.8468 (mmp) outliers start: 33 outliers final: 28 residues processed: 155 average time/residue: 0.2005 time to fit residues: 43.0014 Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8911 Z= 0.213 Angle : 0.513 8.483 12116 Z= 0.271 Chirality : 0.042 0.145 1409 Planarity : 0.003 0.042 1519 Dihedral : 4.268 36.849 1245 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.00 % Allowed : 19.89 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.15 (0.25), residues: 1128 helix: 1.83 (0.28), residues: 393 sheet: -0.26 (0.31), residues: 253 loop : -1.15 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR H 190 ARG 0.010 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.960 Fit side-chains REVERT: A 280 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.8047 (ttp80) REVERT: B 59 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: C 21 MET cc_start: 0.8647 (tmm) cc_final: 0.8444 (tmm) REVERT: C 47 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7477 (mp0) REVERT: H 71 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7205 (p) REVERT: R 74 LEU cc_start: 0.8806 (mp) cc_final: 0.8572 (mt) REVERT: R 98 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7384 (mp) REVERT: R 122 PHE cc_start: 0.6713 (m-80) cc_final: 0.6428 (m-80) REVERT: R 184 MET cc_start: 0.8247 (mmt) cc_final: 0.7379 (mtp) REVERT: R 191 MET cc_start: 0.8736 (mmt) cc_final: 0.8472 (mmp) outliers start: 36 outliers final: 33 residues processed: 150 average time/residue: 0.2060 time to fit residues: 42.7612 Evaluate side-chains 161 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 106 optimal weight: 7.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8911 Z= 0.132 Angle : 0.491 9.480 12116 Z= 0.254 Chirality : 0.041 0.138 1409 Planarity : 0.003 0.048 1519 Dihedral : 4.064 36.717 1245 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.78 % Allowed : 20.22 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.28 (0.25), residues: 1128 helix: 1.93 (0.28), residues: 393 sheet: -0.37 (0.30), residues: 270 loop : -0.95 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR H 190 ARG 0.011 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.941 Fit side-chains REVERT: A 280 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.8006 (ttp80) REVERT: B 59 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: C 47 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7487 (mp0) REVERT: H 71 SER cc_start: 0.7485 (OUTLIER) cc_final: 0.7152 (p) REVERT: R 74 LEU cc_start: 0.8804 (mp) cc_final: 0.8555 (mt) REVERT: R 98 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7358 (mp) REVERT: R 122 PHE cc_start: 0.6665 (m-80) cc_final: 0.6398 (m-80) REVERT: R 151 ASP cc_start: 0.8136 (t70) cc_final: 0.7420 (t0) REVERT: R 184 MET cc_start: 0.8210 (mmt) cc_final: 0.7390 (mtp) REVERT: R 191 MET cc_start: 0.8806 (mmt) cc_final: 0.8527 (mmp) outliers start: 34 outliers final: 26 residues processed: 153 average time/residue: 0.2047 time to fit residues: 43.4600 Evaluate side-chains 160 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8911 Z= 0.196 Angle : 0.528 9.207 12116 Z= 0.273 Chirality : 0.042 0.145 1409 Planarity : 0.003 0.050 1519 Dihedral : 4.115 36.262 1243 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.44 % Allowed : 20.78 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1128 helix: 1.92 (0.27), residues: 393 sheet: -0.23 (0.31), residues: 258 loop : -1.00 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR H 190 ARG 0.012 0.000 ARG R 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.990 Fit side-chains REVERT: A 280 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8000 (ttp80) REVERT: B 59 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: C 47 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7499 (mp0) REVERT: H 71 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7193 (p) REVERT: R 98 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7355 (mp) REVERT: R 122 PHE cc_start: 0.6681 (m-80) cc_final: 0.6420 (m-80) REVERT: R 184 MET cc_start: 0.8179 (mmt) cc_final: 0.7358 (mtp) REVERT: R 191 MET cc_start: 0.8803 (mmt) cc_final: 0.8395 (mmp) REVERT: L 28 MET cc_start: 0.8102 (mmm) cc_final: 0.7617 (mmt) outliers start: 31 outliers final: 27 residues processed: 145 average time/residue: 0.2103 time to fit residues: 42.0884 Evaluate side-chains 156 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 24 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119222 restraints weight = 11517.415| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.63 r_work: 0.3516 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8911 Z= 0.152 Angle : 0.511 9.123 12116 Z= 0.262 Chirality : 0.041 0.140 1409 Planarity : 0.003 0.050 1519 Dihedral : 4.019 36.417 1243 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.44 % Allowed : 20.78 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1128 helix: 1.95 (0.27), residues: 393 sheet: -0.28 (0.30), residues: 270 loop : -0.86 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR H 190 ARG 0.012 0.000 ARG R 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.69 seconds wall clock time: 40 minutes 3.22 seconds (2403.22 seconds total)