Starting phenix.real_space_refine on Mon Mar 11 14:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn1_29303/03_2024/8fn1_29303.pdb" } resolution = 2.88 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= 0.002 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 56 5.16 5 C 5375 2.51 5 N 1418 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 8": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8444 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2027 Classifications: {'peptide': 278} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2552 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 381 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1759 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.98, per 1000 atoms: 0.59 Number of scatterers: 8444 At special positions: 0 Unit cell: (93.28, 118.8, 132.88, 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 56 16.00 O 1595 8.00 N 1418 7.00 C 5375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 37.2% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 60 through 90 removed outlier: 3.520A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 128 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 137 through 173 Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.819A pdb=" N THR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.962A pdb=" N VAL A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 267 Processing helix chain 'A' and resid 302 through 320 removed outlier: 3.592A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.780A pdb=" N HIS A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 371 removed outlier: 3.585A pdb=" N HIS A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'B' and resid 3 through 29 removed outlier: 3.900A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.965A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.933A pdb=" N ILE B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.511A pdb=" N ALA B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 223 removed outlier: 3.562A pdb=" N VAL B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.886A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.734A pdb=" N ALA B 102 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.581A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.628A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.945A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.636A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.675A pdb=" N GLY C 202 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 217 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.509A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.593A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.915A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.915A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.450A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.099A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1281 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: 2.75 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1390 1.32 - 1.44: 2367 1.44 - 1.56: 4781 1.56 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8619 Sorted by residual: bond pdb=" C ILE A 70 " pdb=" O ILE A 70 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.09e-02 8.42e+03 1.35e+01 bond pdb=" N ASN B 75 " pdb=" CA ASN B 75 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.28e-02 6.10e+03 9.97e+00 bond pdb=" C LYS A 64 " pdb=" O LYS A 64 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.32e-02 5.74e+03 8.70e+00 bond pdb=" C VAL A 67 " pdb=" O VAL A 67 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 8.02e+00 bond pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta sigma weight residual 1.461 1.500 -0.040 1.42e-02 4.96e+03 7.85e+00 ... (remaining 8614 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 241 107.21 - 113.90: 4859 113.90 - 120.59: 3399 120.59 - 127.29: 3121 127.29 - 133.98: 92 Bond angle restraints: 11712 Sorted by residual: angle pdb=" N THR A 68 " pdb=" CA THR A 68 " pdb=" C THR A 68 " ideal model delta sigma weight residual 111.28 103.13 8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 110.62 105.11 5.51 1.02e+00 9.61e-01 2.92e+01 angle pdb=" CA ILE A 70 " pdb=" CB ILE A 70 " pdb=" CG2 ILE A 70 " ideal model delta sigma weight residual 110.50 119.66 -9.16 1.70e+00 3.46e-01 2.90e+01 angle pdb=" CA ILE A 70 " pdb=" CB ILE A 70 " pdb=" CG1 ILE A 70 " ideal model delta sigma weight residual 110.40 118.94 -8.54 1.70e+00 3.46e-01 2.52e+01 angle pdb=" N VAL A 67 " pdb=" CA VAL A 67 " pdb=" CB VAL A 67 " ideal model delta sigma weight residual 110.54 117.02 -6.48 1.36e+00 5.41e-01 2.27e+01 ... (remaining 11707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 4865 16.30 - 32.59: 154 32.59 - 48.89: 24 48.89 - 65.18: 9 65.18 - 81.48: 3 Dihedral angle restraints: 5055 sinusoidal: 1841 harmonic: 3214 Sorted by residual: dihedral pdb=" CA HIS B 116 " pdb=" C HIS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 1354 0.352 - 0.704: 0 0.704 - 1.056: 0 1.056 - 1.408: 0 1.408 - 1.760: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CB ILE A 70 " pdb=" CA ILE A 70 " pdb=" CG1 ILE A 70 " pdb=" CG2 ILE A 70 " both_signs ideal model delta sigma weight residual False 2.64 0.88 1.76 2.00e-01 2.50e+01 7.74e+01 chirality pdb=" CA VAL A 65 " pdb=" N VAL A 65 " pdb=" C VAL A 65 " pdb=" CB VAL A 65 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1352 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 68 " -0.012 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C THR A 68 " 0.044 2.00e-02 2.50e+03 pdb=" O THR A 68 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 69 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 314 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C VAL A 314 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 314 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 315 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 74 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS B 74 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS B 74 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN B 75 " -0.009 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 370 2.72 - 3.26: 8530 3.26 - 3.81: 13844 3.81 - 4.35: 17424 4.35 - 4.90: 30268 Nonbonded interactions: 70436 Sorted by model distance: nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.173 2.440 nonbonded pdb=" O GLY E 197 " pdb=" OG1 THR E 198 " model vdw 2.190 2.440 nonbonded pdb=" OG SER A 108 " pdb=" OD1 ASN A 159 " model vdw 2.200 2.440 nonbonded pdb=" O MET C 325 " pdb=" ND2 ASN C 340 " model vdw 2.227 2.520 nonbonded pdb=" OD2 ASP E 73 " pdb=" NZ LYS E 76 " model vdw 2.241 2.520 ... (remaining 70431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 3.820 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.820 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.004 0.040 8619 Z= 0.246 Angle : 0.589 9.158 11712 Z= 0.375 Chirality : 0.063 1.760 1355 Planarity : 0.003 0.030 1486 Dihedral : 9.146 81.475 2981 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.23 % Allowed : 1.70 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.17 (0.26), residues: 1094 helix: 2.16 (0.28), residues: 362 sheet: 0.59 (0.28), residues: 292 loop : -0.21 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE B 73 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG F 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 0.941 Fit side-chains REVERT: A 169 LEU cc_start: 0.8015 (tp) cc_final: 0.7814 (tp) REVERT: A 309 VAL cc_start: 0.7218 (t) cc_final: 0.6786 (p) REVERT: A 343 LEU cc_start: 0.7396 (mt) cc_final: 0.7168 (mt) REVERT: A 347 TYR cc_start: 0.6992 (t80) cc_final: 0.6777 (t80) REVERT: A 364 ILE cc_start: 0.7576 (mt) cc_final: 0.7278 (mt) REVERT: B 30 ASP cc_start: 0.7495 (m-30) cc_final: 0.7289 (m-30) REVERT: B 111 ASP cc_start: 0.7661 (t0) cc_final: 0.7123 (t0) REVERT: B 120 MET cc_start: 0.7091 (mmm) cc_final: 0.6865 (mmm) REVERT: C 52 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7076 (mtt90) REVERT: C 97 SER cc_start: 0.8467 (t) cc_final: 0.8044 (p) REVERT: C 268 ASN cc_start: 0.6769 (p0) cc_final: 0.6483 (p0) REVERT: E 7 SER cc_start: 0.8249 (t) cc_final: 0.8003 (m) outliers start: 2 outliers final: 0 residues processed: 190 average time/residue: 0.7360 time to fit residues: 153.9875 Evaluate side-chains 158 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 128 ASN B 193 HIS C 62 HIS C 110 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8619 Z= 0.183 Angle : 0.493 6.923 11712 Z= 0.267 Chirality : 0.042 0.170 1355 Planarity : 0.003 0.036 1486 Dihedral : 4.289 21.241 1188 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.49 % Allowed : 9.05 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.33 (0.25), residues: 1094 helix: 2.40 (0.27), residues: 367 sheet: 0.65 (0.28), residues: 273 loop : -0.19 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 321 HIS 0.003 0.001 HIS E 35 PHE 0.024 0.002 PHE B 73 TYR 0.023 0.002 TYR A 71 ARG 0.006 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.7097 (mmp) cc_final: 0.6780 (mpm) REVERT: A 237 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7518 (t) REVERT: A 343 LEU cc_start: 0.7287 (mt) cc_final: 0.7084 (mt) REVERT: A 364 ILE cc_start: 0.7645 (mt) cc_final: 0.7390 (mt) REVERT: B 77 HIS cc_start: 0.8072 (t-170) cc_final: 0.7745 (t70) REVERT: B 111 ASP cc_start: 0.7826 (t0) cc_final: 0.7323 (t0) REVERT: C 51 LEU cc_start: 0.8559 (mt) cc_final: 0.8284 (mm) REVERT: C 52 ARG cc_start: 0.7355 (mtt90) cc_final: 0.7139 (mtt90) REVERT: C 97 SER cc_start: 0.8430 (t) cc_final: 0.8203 (p) REVERT: C 186 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: C 198 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8026 (pt) REVERT: C 268 ASN cc_start: 0.6815 (p0) cc_final: 0.6574 (p0) REVERT: C 274 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7916 (p) REVERT: C 318 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8189 (tp) REVERT: E 7 SER cc_start: 0.8164 (t) cc_final: 0.7910 (m) REVERT: E 93 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8173 (ttt) outliers start: 22 outliers final: 6 residues processed: 161 average time/residue: 0.7341 time to fit residues: 130.5738 Evaluate side-chains 164 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 133 HIS B 70 HIS B 128 ASN C 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8619 Z= 0.228 Angle : 0.491 5.239 11712 Z= 0.264 Chirality : 0.042 0.132 1355 Planarity : 0.004 0.039 1486 Dihedral : 4.274 20.445 1188 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.39 % Allowed : 9.62 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1094 helix: 2.46 (0.28), residues: 366 sheet: 0.65 (0.29), residues: 279 loop : -0.20 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 321 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE C 151 TYR 0.016 0.002 TYR A 359 ARG 0.004 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 0.960 Fit side-chains REVERT: A 146 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5750 (t80) REVERT: A 204 MET cc_start: 0.7151 (mmp) cc_final: 0.6761 (mpm) REVERT: A 229 VAL cc_start: 0.7941 (t) cc_final: 0.7728 (p) REVERT: A 237 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7478 (p) REVERT: A 364 ILE cc_start: 0.7617 (mt) cc_final: 0.7374 (mt) REVERT: B 111 ASP cc_start: 0.7802 (t0) cc_final: 0.7354 (t0) REVERT: C 51 LEU cc_start: 0.8545 (mt) cc_final: 0.8319 (mm) REVERT: C 52 ARG cc_start: 0.7357 (mtt90) cc_final: 0.7144 (mtt90) REVERT: C 97 SER cc_start: 0.8390 (t) cc_final: 0.8134 (p) REVERT: C 268 ASN cc_start: 0.6833 (p0) cc_final: 0.6613 (p0) REVERT: C 318 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8273 (tp) REVERT: E 7 SER cc_start: 0.8216 (t) cc_final: 0.7995 (m) REVERT: E 93 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (ttt) outliers start: 30 outliers final: 16 residues processed: 162 average time/residue: 0.7386 time to fit residues: 132.0145 Evaluate side-chains 168 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8619 Z= 0.273 Angle : 0.513 5.326 11712 Z= 0.274 Chirality : 0.042 0.130 1355 Planarity : 0.004 0.040 1486 Dihedral : 4.350 20.716 1188 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.39 % Allowed : 9.84 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.25 (0.26), residues: 1094 helix: 2.32 (0.28), residues: 369 sheet: 0.66 (0.29), residues: 274 loop : -0.27 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 321 HIS 0.005 0.001 HIS E 35 PHE 0.018 0.002 PHE C 151 TYR 0.015 0.002 TYR E 178 ARG 0.004 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.971 Fit side-chains REVERT: A 146 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5732 (t80) REVERT: A 204 MET cc_start: 0.7221 (mmp) cc_final: 0.6840 (mpm) REVERT: A 229 VAL cc_start: 0.7943 (t) cc_final: 0.7728 (p) REVERT: A 237 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7498 (p) REVERT: A 309 VAL cc_start: 0.7413 (t) cc_final: 0.7042 (p) REVERT: A 329 LEU cc_start: 0.7126 (mt) cc_final: 0.6876 (mm) REVERT: A 347 TYR cc_start: 0.6793 (t80) cc_final: 0.6570 (t80) REVERT: A 364 ILE cc_start: 0.7624 (mt) cc_final: 0.7382 (mt) REVERT: B 111 ASP cc_start: 0.7794 (t0) cc_final: 0.7332 (t0) REVERT: B 142 LYS cc_start: 0.8035 (mttt) cc_final: 0.7706 (ptmt) REVERT: C 51 LEU cc_start: 0.8529 (mt) cc_final: 0.8323 (mm) REVERT: C 52 ARG cc_start: 0.7337 (mtt90) cc_final: 0.7129 (mtt90) REVERT: C 97 SER cc_start: 0.8383 (t) cc_final: 0.8125 (p) REVERT: C 197 ARG cc_start: 0.7235 (ttm170) cc_final: 0.7028 (mtm180) REVERT: C 198 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (pt) REVERT: C 217 MET cc_start: 0.8169 (ptm) cc_final: 0.7968 (ptm) REVERT: C 268 ASN cc_start: 0.6807 (p0) cc_final: 0.6598 (p0) REVERT: E 7 SER cc_start: 0.8213 (t) cc_final: 0.7986 (m) REVERT: E 93 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8221 (ttt) outliers start: 30 outliers final: 17 residues processed: 160 average time/residue: 0.7555 time to fit residues: 133.2622 Evaluate side-chains 173 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8619 Z= 0.190 Angle : 0.465 5.308 11712 Z= 0.250 Chirality : 0.041 0.126 1355 Planarity : 0.003 0.040 1486 Dihedral : 4.147 19.243 1188 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.39 % Allowed : 11.09 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.34 (0.26), residues: 1094 helix: 2.41 (0.28), residues: 369 sheet: 0.69 (0.30), residues: 274 loop : -0.24 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.014 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 67 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6631 (p) REVERT: A 146 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5824 (t80) REVERT: A 204 MET cc_start: 0.7130 (mmp) cc_final: 0.6815 (mpm) REVERT: A 237 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7537 (p) REVERT: A 309 VAL cc_start: 0.7393 (t) cc_final: 0.7049 (p) REVERT: A 329 LEU cc_start: 0.7095 (mt) cc_final: 0.6858 (mm) REVERT: A 359 TYR cc_start: 0.7063 (m-80) cc_final: 0.6798 (m-10) REVERT: A 364 ILE cc_start: 0.7606 (mt) cc_final: 0.7375 (mt) REVERT: B 111 ASP cc_start: 0.7793 (t0) cc_final: 0.7372 (t0) REVERT: C 97 SER cc_start: 0.8376 (t) cc_final: 0.8098 (p) REVERT: C 197 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6972 (mtm180) REVERT: C 198 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8023 (pt) REVERT: C 262 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7355 (tpp) REVERT: C 268 ASN cc_start: 0.6810 (p0) cc_final: 0.6607 (p0) REVERT: E 7 SER cc_start: 0.8195 (t) cc_final: 0.7983 (m) REVERT: E 93 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8247 (ttt) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.7017 time to fit residues: 128.6898 Evaluate side-chains 172 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0060 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 0.0670 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8619 Z= 0.156 Angle : 0.456 6.444 11712 Z= 0.248 Chirality : 0.041 0.142 1355 Planarity : 0.003 0.039 1486 Dihedral : 3.994 18.630 1188 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.39 % Allowed : 11.76 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.48 (0.26), residues: 1094 helix: 2.57 (0.28), residues: 370 sheet: 0.72 (0.30), residues: 274 loop : -0.17 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.025 0.001 PHE A 331 TYR 0.014 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6587 (m) REVERT: A 146 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.5810 (t80) REVERT: A 237 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7543 (p) REVERT: A 364 ILE cc_start: 0.7516 (mt) cc_final: 0.7273 (mt) REVERT: B 111 ASP cc_start: 0.7805 (t0) cc_final: 0.7362 (t0) REVERT: C 97 SER cc_start: 0.8376 (t) cc_final: 0.8144 (p) REVERT: C 197 ARG cc_start: 0.7054 (ttm170) cc_final: 0.6828 (mtm180) REVERT: C 198 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (pt) REVERT: C 262 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7379 (tpp) REVERT: E 7 SER cc_start: 0.8112 (t) cc_final: 0.7899 (m) REVERT: E 93 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (ttt) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.7681 time to fit residues: 132.0526 Evaluate side-chains 166 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8619 Z= 0.171 Angle : 0.468 10.170 11712 Z= 0.249 Chirality : 0.041 0.145 1355 Planarity : 0.003 0.039 1486 Dihedral : 3.966 18.595 1188 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.17 % Allowed : 13.24 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.54 (0.26), residues: 1094 helix: 2.62 (0.28), residues: 371 sheet: 0.75 (0.30), residues: 274 loop : -0.15 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 331 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 146 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.5876 (t80) REVERT: A 237 VAL cc_start: 0.7772 (p) cc_final: 0.7539 (p) REVERT: A 309 VAL cc_start: 0.7316 (t) cc_final: 0.6991 (p) REVERT: A 364 ILE cc_start: 0.7527 (mt) cc_final: 0.7278 (mt) REVERT: B 111 ASP cc_start: 0.7767 (t0) cc_final: 0.7374 (t0) REVERT: C 97 SER cc_start: 0.8371 (t) cc_final: 0.8134 (p) REVERT: C 197 ARG cc_start: 0.7091 (ttm170) cc_final: 0.6847 (mtm180) REVERT: C 198 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8044 (pt) REVERT: C 262 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7375 (tpp) REVERT: E 7 SER cc_start: 0.8158 (t) cc_final: 0.7953 (m) REVERT: E 93 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (ttt) outliers start: 28 outliers final: 20 residues processed: 162 average time/residue: 0.6925 time to fit residues: 124.6254 Evaluate side-chains 178 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8619 Z= 0.218 Angle : 0.481 5.841 11712 Z= 0.256 Chirality : 0.041 0.136 1355 Planarity : 0.004 0.066 1486 Dihedral : 4.098 19.658 1188 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.28 % Allowed : 14.14 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.50 (0.26), residues: 1094 helix: 2.59 (0.27), residues: 371 sheet: 0.74 (0.30), residues: 274 loop : -0.17 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.017 0.001 TYR A 71 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6335 (tp) cc_final: 0.6106 (tp) REVERT: A 146 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5837 (t80) REVERT: A 309 VAL cc_start: 0.7376 (t) cc_final: 0.7017 (p) REVERT: A 350 PHE cc_start: 0.6814 (t80) cc_final: 0.6601 (t80) REVERT: A 364 ILE cc_start: 0.7556 (mt) cc_final: 0.7293 (mt) REVERT: B 111 ASP cc_start: 0.7818 (t0) cc_final: 0.7409 (t0) REVERT: C 97 SER cc_start: 0.8365 (t) cc_final: 0.8122 (p) REVERT: C 197 ARG cc_start: 0.7112 (ttm170) cc_final: 0.6848 (mtm180) REVERT: C 198 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8034 (pt) REVERT: C 262 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7371 (tpp) REVERT: E 7 SER cc_start: 0.8205 (t) cc_final: 0.7995 (m) REVERT: E 93 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8224 (ttt) outliers start: 29 outliers final: 19 residues processed: 158 average time/residue: 0.7043 time to fit residues: 123.4347 Evaluate side-chains 170 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8619 Z= 0.209 Angle : 0.492 11.074 11712 Z= 0.259 Chirality : 0.041 0.152 1355 Planarity : 0.004 0.065 1486 Dihedral : 4.125 19.747 1188 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 15.16 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.49 (0.26), residues: 1094 helix: 2.63 (0.27), residues: 369 sheet: 0.72 (0.30), residues: 274 loop : -0.21 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6328 (tp) cc_final: 0.6081 (tp) REVERT: A 146 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.5826 (t80) REVERT: A 309 VAL cc_start: 0.7394 (t) cc_final: 0.7028 (p) REVERT: A 364 ILE cc_start: 0.7572 (mt) cc_final: 0.7288 (mt) REVERT: B 111 ASP cc_start: 0.7821 (t0) cc_final: 0.7409 (t0) REVERT: C 51 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8152 (mt) REVERT: C 97 SER cc_start: 0.8361 (t) cc_final: 0.8120 (p) REVERT: C 197 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6845 (mtm180) REVERT: C 198 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8041 (pt) REVERT: C 262 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7369 (tpp) REVERT: E 7 SER cc_start: 0.8202 (t) cc_final: 0.7987 (m) REVERT: E 93 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8215 (ttt) outliers start: 27 outliers final: 19 residues processed: 160 average time/residue: 0.7082 time to fit residues: 125.7430 Evaluate side-chains 173 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8619 Z= 0.219 Angle : 0.486 7.587 11712 Z= 0.260 Chirality : 0.041 0.133 1355 Planarity : 0.004 0.064 1486 Dihedral : 4.128 20.053 1188 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.94 % Allowed : 15.27 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.50 (0.26), residues: 1094 helix: 2.62 (0.27), residues: 372 sheet: 0.64 (0.30), residues: 276 loop : -0.14 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 321 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 146 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5828 (t80) REVERT: A 229 VAL cc_start: 0.8174 (m) cc_final: 0.7964 (p) REVERT: A 309 VAL cc_start: 0.7407 (t) cc_final: 0.7044 (p) REVERT: A 359 TYR cc_start: 0.6982 (m-80) cc_final: 0.6714 (m-10) REVERT: A 361 SER cc_start: 0.6899 (OUTLIER) cc_final: 0.6387 (p) REVERT: A 364 ILE cc_start: 0.7575 (mt) cc_final: 0.7299 (mt) REVERT: B 111 ASP cc_start: 0.7755 (t0) cc_final: 0.7362 (t0) REVERT: C 97 SER cc_start: 0.8362 (t) cc_final: 0.8118 (p) REVERT: C 197 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6861 (mtm180) REVERT: C 198 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8034 (pt) REVERT: E 7 SER cc_start: 0.8208 (t) cc_final: 0.7991 (m) REVERT: E 93 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8222 (ttt) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.6978 time to fit residues: 130.0129 Evaluate side-chains 179 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 0.0770 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120961 restraints weight = 12301.066| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.97 r_work: 0.3448 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8619 Z= 0.160 Angle : 0.472 7.560 11712 Z= 0.249 Chirality : 0.040 0.130 1355 Planarity : 0.004 0.061 1486 Dihedral : 3.954 18.231 1188 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.49 % Allowed : 16.29 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.55 (0.26), residues: 1094 helix: 2.65 (0.27), residues: 370 sheet: 0.76 (0.30), residues: 273 loop : -0.15 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 105 PHE 0.012 0.001 PHE C 199 TYR 0.012 0.001 TYR E 178 ARG 0.002 0.000 ARG F 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.38 seconds wall clock time: 56 minutes 30.48 seconds (3390.48 seconds total)