Starting phenix.real_space_refine on Mon Mar 11 17:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/03_2024/8fmz_29301.pdb" } resolution = 2.59 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= 0.159 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 55 5.16 5 C 5595 2.51 5 N 1492 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "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 "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1795 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 380 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1754 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2188 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 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} Time building chain proxies: 5.24, per 1000 atoms: 0.60 Number of scatterers: 8768 At special positions: 0 Unit cell: (88.88, 120.56, 131.12, 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 55 16.00 O 1626 8.00 N 1492 7.00 C 5595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 94 through 101 removed outlier: 3.736A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.079A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.505A pdb=" N TYR B 170 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.738A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 37 removed outlier: 4.078A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.775A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.312A 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 53 through 56 removed outlier: 4.166A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 52 through 56 removed outlier: 4.040A pdb=" N ASP A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 Processing helix chain 'A' and resid 101 through 128 removed outlier: 3.679A pdb=" N HIS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) 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: 3.579A pdb=" N THR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.543A pdb=" N ALA A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.618A pdb=" N VAL A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 266 Processing helix chain 'A' and resid 304 through 334 Proline residue: A 323 - end of helix removed outlier: 3.552A pdb=" N ILE A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 370 removed outlier: 3.671A pdb=" N HIS A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.697A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.711A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.566A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.915A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.669A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.550A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 208 through 212 471 hydrogen bonds defined for protein. 1287 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: 2.71 Time building geometry restraints manager: 3.58 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: 2822 1.34 - 1.46: 2052 1.46 - 1.58: 3998 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8953 Sorted by residual: bond pdb=" N ASP C 291 " pdb=" CA ASP C 291 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.40e-02 5.10e+03 6.68e+00 bond pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.32e-02 5.74e+03 5.59e+00 bond pdb=" N ASP C 186 " pdb=" CA ASP C 186 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.28e-02 6.10e+03 5.43e+00 bond pdb=" C ILE A 202 " pdb=" N PRO A 203 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.16e+00 bond pdb=" CA ASP C 290 " pdb=" C ASP C 290 " ideal model delta sigma weight residual 1.523 1.539 -0.017 1.41e-02 5.03e+03 1.42e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.38: 206 106.38 - 113.29: 4882 113.29 - 120.20: 3128 120.20 - 127.11: 3826 127.11 - 134.02: 100 Bond angle restraints: 12142 Sorted by residual: angle pdb=" N VAL C 187 " pdb=" CA VAL C 187 " pdb=" CB VAL C 187 " ideal model delta sigma weight residual 111.00 119.79 -8.79 1.14e+00 7.69e-01 5.95e+01 angle pdb=" N TYR C 289 " pdb=" CA TYR C 289 " pdb=" C TYR C 289 " ideal model delta sigma weight residual 109.81 118.54 -8.73 1.53e+00 4.27e-01 3.26e+01 angle pdb=" N VAL C 187 " pdb=" CA VAL C 187 " pdb=" C VAL C 187 " ideal model delta sigma weight residual 108.23 103.12 5.11 1.53e+00 4.27e-01 1.12e+01 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 122.40 126.46 -4.06 1.45e+00 4.76e-01 7.84e+00 angle pdb=" CA ASP C 186 " pdb=" C ASP C 186 " pdb=" O ASP C 186 " ideal model delta sigma weight residual 120.92 117.93 2.99 1.14e+00 7.69e-01 6.87e+00 ... (remaining 12137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 5047 15.83 - 31.67: 207 31.67 - 47.50: 27 47.50 - 63.34: 4 63.34 - 79.17: 2 Dihedral angle restraints: 5287 sinusoidal: 2020 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+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 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+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 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 991 0.041 - 0.082: 307 0.082 - 0.124: 86 0.124 - 0.165: 3 0.165 - 0.206: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA TYR C 289 " pdb=" N TYR C 289 " pdb=" C TYR C 289 " pdb=" CB TYR C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 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 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1385 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 289 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C TYR C 289 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR C 289 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP C 290 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO C 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 226 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 227 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.020 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2006 2.79 - 3.32: 8111 3.32 - 3.85: 14475 3.85 - 4.37: 17461 4.37 - 4.90: 30600 Nonbonded interactions: 72653 Sorted by model distance: nonbonded pdb=" OE2 GLU C 260 " pdb=" OG1 THR C 263 " model vdw 2.264 2.440 nonbonded pdb=" O ASN A 241 " pdb=" OG SER A 245 " model vdw 2.267 2.440 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.269 2.440 nonbonded pdb=" O ASP A 230 " pdb=" OG1 THR A 233 " model vdw 2.273 2.440 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.275 2.520 ... (remaining 72648 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=0.00 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: 1.030 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: 4.410 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 0.036 8953 Z= 0.263 Angle : 0.575 8.795 12142 Z= 0.346 Chirality : 0.042 0.206 1388 Planarity : 0.004 0.044 1531 Dihedral : 8.857 79.171 3171 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.58 (0.25), residues: 1098 helix: 2.54 (0.26), residues: 381 sheet: 0.65 (0.28), residues: 301 loop : 0.01 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 0.893 Fit side-chains REVERT: B 10 LYS cc_start: 0.7671 (mttt) cc_final: 0.7282 (mttt) REVERT: B 21 LYS cc_start: 0.7549 (tttm) cc_final: 0.6884 (ttpt) REVERT: B 24 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6116 (mtm-85) REVERT: B 69 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 120 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 195 LYS cc_start: 0.7358 (tttm) cc_final: 0.7113 (ttpp) REVERT: B 208 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6567 (ptt-90) REVERT: C 101 MET cc_start: 0.8277 (mtt) cc_final: 0.8063 (mpp) REVERT: C 254 ASP cc_start: 0.7683 (t70) cc_final: 0.7377 (t0) REVERT: C 325 MET cc_start: 0.8036 (mmm) cc_final: 0.7719 (tpp) REVERT: D 21 MET cc_start: 0.6224 (mtm) cc_final: 0.5483 (tmm) REVERT: E 7 SER cc_start: 0.8016 (t) cc_final: 0.7605 (p) REVERT: E 46 GLU cc_start: 0.7617 (tt0) cc_final: 0.7169 (tt0) REVERT: E 85 SER cc_start: 0.8216 (m) cc_final: 0.7899 (t) REVERT: A 61 ILE cc_start: 0.5555 (tp) cc_final: 0.5323 (tp) REVERT: A 121 MET cc_start: 0.6297 (tpp) cc_final: 0.6066 (tpp) REVERT: A 248 PHE cc_start: 0.7530 (t80) cc_final: 0.7284 (t80) REVERT: A 361 SER cc_start: 0.7548 (t) cc_final: 0.7050 (p) outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 1.1573 time to fit residues: 255.6981 Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 62 HIS C 132 ASN C 340 ASN E 130 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8953 Z= 0.201 Angle : 0.513 5.995 12142 Z= 0.279 Chirality : 0.042 0.127 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.344 22.722 1219 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 10.64 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.65 (0.25), residues: 1098 helix: 2.52 (0.26), residues: 388 sheet: 0.73 (0.29), residues: 288 loop : 0.06 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS D 44 PHE 0.019 0.001 PHE C 151 TYR 0.013 0.002 TYR E 178 ARG 0.007 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.078 Fit side-chains REVERT: B 10 LYS cc_start: 0.7790 (mttt) cc_final: 0.7295 (mttt) REVERT: B 21 LYS cc_start: 0.7592 (tttm) cc_final: 0.6933 (ttpt) REVERT: B 24 ARG cc_start: 0.6581 (mtm-85) cc_final: 0.6203 (mtm-85) REVERT: B 120 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 135 ARG cc_start: 0.7922 (ptp-110) cc_final: 0.7717 (ptp-110) REVERT: B 151 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6296 (pt0) REVERT: B 195 LYS cc_start: 0.7345 (tttm) cc_final: 0.7051 (ttpp) REVERT: B 208 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6524 (ptt-90) REVERT: B 232 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7850 (ttpt) REVERT: C 219 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7328 (mtp180) REVERT: C 247 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: C 254 ASP cc_start: 0.7732 (t70) cc_final: 0.7524 (t0) REVERT: D 21 MET cc_start: 0.6160 (mtm) cc_final: 0.5450 (tmt) REVERT: E 7 SER cc_start: 0.8054 (t) cc_final: 0.7582 (p) REVERT: E 43 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7243 (mtpm) REVERT: E 46 GLU cc_start: 0.8303 (tt0) cc_final: 0.7799 (tt0) REVERT: E 85 SER cc_start: 0.8392 (m) cc_final: 0.7982 (p) REVERT: A 121 MET cc_start: 0.6205 (tpp) cc_final: 0.6004 (tpp) REVERT: A 248 PHE cc_start: 0.7434 (t80) cc_final: 0.7176 (t80) outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 1.3946 time to fit residues: 231.5538 Evaluate side-chains 136 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 174 GLN E 182 ASN A 52 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 8953 Z= 0.425 Angle : 0.650 8.787 12142 Z= 0.350 Chirality : 0.047 0.146 1388 Planarity : 0.005 0.058 1531 Dihedral : 4.934 23.831 1217 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.51 % Allowed : 11.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1098 helix: 2.22 (0.26), residues: 382 sheet: 0.51 (0.28), residues: 298 loop : -0.16 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.005 0.002 HIS B 82 PHE 0.025 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.006 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.023 Fit side-chains REVERT: B 10 LYS cc_start: 0.7834 (mttt) cc_final: 0.7257 (mttt) REVERT: B 21 LYS cc_start: 0.7686 (tttm) cc_final: 0.7042 (ttpt) REVERT: B 24 ARG cc_start: 0.6652 (mtm-85) cc_final: 0.6332 (mtm-85) REVERT: B 120 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7040 (mt-10) REVERT: B 135 ARG cc_start: 0.8083 (ptp-110) cc_final: 0.7820 (ptp-110) REVERT: B 195 LYS cc_start: 0.7412 (tttm) cc_final: 0.7111 (ttpp) REVERT: B 232 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7894 (ttpt) REVERT: C 217 MET cc_start: 0.8221 (pmm) cc_final: 0.7973 (pmm) REVERT: C 219 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7394 (mtp180) REVERT: D 21 MET cc_start: 0.6260 (mtm) cc_final: 0.5502 (tmt) REVERT: E 7 SER cc_start: 0.8096 (t) cc_final: 0.7595 (p) REVERT: E 43 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7307 (mtpm) REVERT: E 46 GLU cc_start: 0.8402 (tt0) cc_final: 0.8140 (tt0) REVERT: E 85 SER cc_start: 0.8487 (m) cc_final: 0.8125 (t) REVERT: A 61 ILE cc_start: 0.5539 (tp) cc_final: 0.5326 (tp) REVERT: A 248 PHE cc_start: 0.7598 (t80) cc_final: 0.7345 (t80) outliers start: 33 outliers final: 23 residues processed: 153 average time/residue: 1.3907 time to fit residues: 225.0684 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 266 HIS A 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8953 Z= 0.199 Angle : 0.510 6.274 12142 Z= 0.277 Chirality : 0.041 0.125 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.472 23.319 1217 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 14.79 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.25), residues: 1098 helix: 2.57 (0.26), residues: 380 sheet: 0.56 (0.29), residues: 287 loop : -0.10 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE C 199 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.973 Fit side-chains REVERT: B 10 LYS cc_start: 0.7713 (mttt) cc_final: 0.7179 (mttt) REVERT: B 21 LYS cc_start: 0.7699 (tttm) cc_final: 0.7077 (ttpt) REVERT: B 24 ARG cc_start: 0.6677 (mtm-85) cc_final: 0.6240 (mtm-85) REVERT: B 135 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7710 (ptp-110) REVERT: B 195 LYS cc_start: 0.7330 (tttm) cc_final: 0.6989 (ttpp) REVERT: B 208 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6190 (mmm-85) REVERT: B 232 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7828 (ttpt) REVERT: C 217 MET cc_start: 0.8170 (pmm) cc_final: 0.7761 (pmm) REVERT: C 219 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7338 (mtp180) REVERT: C 247 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: D 21 MET cc_start: 0.6282 (mtm) cc_final: 0.5613 (tmt) REVERT: E 7 SER cc_start: 0.8223 (t) cc_final: 0.7761 (p) REVERT: E 43 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7329 (mtpm) REVERT: E 46 GLU cc_start: 0.8386 (tt0) cc_final: 0.8136 (tt0) REVERT: E 85 SER cc_start: 0.8508 (m) cc_final: 0.8059 (p) REVERT: A 248 PHE cc_start: 0.7458 (t80) cc_final: 0.7184 (t80) outliers start: 31 outliers final: 21 residues processed: 137 average time/residue: 1.4168 time to fit residues: 206.1605 Evaluate side-chains 138 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN A 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8953 Z= 0.236 Angle : 0.522 6.381 12142 Z= 0.282 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.504 23.085 1217 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.57 % Allowed : 13.83 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.46 (0.25), residues: 1098 helix: 2.48 (0.26), residues: 385 sheet: 0.62 (0.29), residues: 287 loop : -0.14 (0.30), residues: 426 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 0.018 0.001 PHE C 151 TYR 0.012 0.002 TYR E 103 ARG 0.006 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 0.983 Fit side-chains REVERT: B 10 LYS cc_start: 0.7764 (mttt) cc_final: 0.7497 (mttm) REVERT: B 21 LYS cc_start: 0.7691 (tttm) cc_final: 0.7082 (ttpt) REVERT: B 24 ARG cc_start: 0.6630 (mtm-85) cc_final: 0.6334 (mtm-85) REVERT: B 135 ARG cc_start: 0.7971 (ptp-110) cc_final: 0.7769 (ptp-110) REVERT: B 195 LYS cc_start: 0.7362 (tttm) cc_final: 0.7018 (ttpp) REVERT: B 232 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7843 (ttpt) REVERT: C 217 MET cc_start: 0.8193 (pmm) cc_final: 0.7765 (pmm) REVERT: C 219 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7333 (mtp180) REVERT: D 21 MET cc_start: 0.6370 (mtm) cc_final: 0.5719 (tmt) REVERT: E 7 SER cc_start: 0.8245 (t) cc_final: 0.7868 (p) REVERT: E 43 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7394 (mtpm) REVERT: E 46 GLU cc_start: 0.8381 (tt0) cc_final: 0.8148 (tt0) REVERT: E 85 SER cc_start: 0.8515 (m) cc_final: 0.8067 (p) REVERT: A 248 PHE cc_start: 0.7496 (t80) cc_final: 0.7198 (t80) outliers start: 43 outliers final: 28 residues processed: 147 average time/residue: 1.2516 time to fit residues: 195.7806 Evaluate side-chains 141 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8953 Z= 0.344 Angle : 0.593 9.207 12142 Z= 0.319 Chirality : 0.044 0.145 1388 Planarity : 0.005 0.045 1531 Dihedral : 4.828 24.461 1217 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.68 % Allowed : 14.04 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.25), residues: 1098 helix: 2.34 (0.26), residues: 381 sheet: 0.47 (0.28), residues: 294 loop : -0.18 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.006 0.001 HIS A 103 PHE 0.021 0.002 PHE C 151 TYR 0.015 0.002 TYR E 103 ARG 0.007 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 0.937 Fit side-chains REVERT: B 10 LYS cc_start: 0.7814 (mttt) cc_final: 0.7225 (mttt) REVERT: B 21 LYS cc_start: 0.7686 (tttm) cc_final: 0.7035 (ttpt) REVERT: B 24 ARG cc_start: 0.6636 (mtm-85) cc_final: 0.6330 (mtm-85) REVERT: B 195 LYS cc_start: 0.7373 (tttm) cc_final: 0.7036 (ttpp) REVERT: B 208 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6198 (mmm-85) REVERT: B 232 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7912 (ttpt) REVERT: C 52 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7648 (mtt90) REVERT: C 217 MET cc_start: 0.8184 (pmm) cc_final: 0.7907 (pmm) REVERT: C 219 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7354 (mtp180) REVERT: C 256 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7597 (mtp180) REVERT: D 21 MET cc_start: 0.6361 (mtm) cc_final: 0.5770 (tmt) REVERT: E 7 SER cc_start: 0.8290 (t) cc_final: 0.7879 (p) REVERT: E 43 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7441 (mtpt) REVERT: E 85 SER cc_start: 0.8504 (m) cc_final: 0.8133 (t) REVERT: A 121 MET cc_start: 0.6004 (tpp) cc_final: 0.5803 (ttp) REVERT: A 248 PHE cc_start: 0.7647 (t80) cc_final: 0.7345 (t80) outliers start: 44 outliers final: 32 residues processed: 142 average time/residue: 1.3263 time to fit residues: 199.9188 Evaluate side-chains 140 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN A 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8953 Z= 0.147 Angle : 0.479 7.676 12142 Z= 0.257 Chirality : 0.040 0.132 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.236 21.996 1217 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.77 % Allowed : 15.74 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.56 (0.26), residues: 1098 helix: 2.58 (0.27), residues: 386 sheet: 0.62 (0.29), residues: 289 loop : -0.07 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 211 HIS 0.004 0.001 HIS A 103 PHE 0.014 0.001 PHE C 199 TYR 0.013 0.001 TYR E 178 ARG 0.008 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.020 Fit side-chains REVERT: B 10 LYS cc_start: 0.7690 (mttt) cc_final: 0.7163 (mttt) REVERT: B 21 LYS cc_start: 0.7660 (tttm) cc_final: 0.7071 (ttpt) REVERT: B 24 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.6312 (mtm-85) REVERT: B 195 LYS cc_start: 0.7339 (tttm) cc_final: 0.6988 (ttpp) REVERT: B 208 ARG cc_start: 0.7070 (mtm110) cc_final: 0.6192 (mmm-85) REVERT: B 232 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7826 (ttpt) REVERT: C 52 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7562 (mtt90) REVERT: C 217 MET cc_start: 0.8180 (pmm) cc_final: 0.7755 (pmm) REVERT: C 219 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7280 (mtp180) REVERT: C 247 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: D 21 MET cc_start: 0.6349 (mtm) cc_final: 0.5750 (tmt) REVERT: E 7 SER cc_start: 0.8191 (t) cc_final: 0.7849 (p) REVERT: E 23 SER cc_start: 0.8364 (t) cc_final: 0.7929 (p) REVERT: E 43 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7365 (mtpm) REVERT: E 85 SER cc_start: 0.8495 (m) cc_final: 0.8046 (p) REVERT: A 248 PHE cc_start: 0.7522 (t80) cc_final: 0.7289 (t80) outliers start: 26 outliers final: 22 residues processed: 138 average time/residue: 1.3770 time to fit residues: 201.2067 Evaluate side-chains 139 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8953 Z= 0.225 Angle : 0.519 7.514 12142 Z= 0.278 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.415 22.703 1217 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.40 % Allowed : 15.43 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1098 helix: 2.53 (0.26), residues: 386 sheet: 0.61 (0.29), residues: 287 loop : -0.08 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE C 151 TYR 0.012 0.002 TYR B 212 ARG 0.006 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.884 Fit side-chains REVERT: B 10 LYS cc_start: 0.7805 (mttt) cc_final: 0.7267 (mttt) REVERT: B 21 LYS cc_start: 0.7686 (tttm) cc_final: 0.7090 (ttpt) REVERT: B 24 ARG cc_start: 0.6613 (mtm-85) cc_final: 0.6304 (mtm-85) REVERT: B 132 ARG cc_start: 0.8337 (ptt-90) cc_final: 0.8017 (ptt-90) REVERT: B 195 LYS cc_start: 0.7366 (tttm) cc_final: 0.7008 (ttpp) REVERT: B 208 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6250 (mmm160) REVERT: B 232 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7855 (ttpt) REVERT: C 52 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7564 (mtt90) REVERT: C 217 MET cc_start: 0.8189 (pmm) cc_final: 0.7751 (pmm) REVERT: C 219 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7308 (mtp180) REVERT: C 247 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: C 256 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7352 (mtp180) REVERT: D 21 MET cc_start: 0.6396 (mtm) cc_final: 0.5782 (tmt) REVERT: E 7 SER cc_start: 0.8195 (t) cc_final: 0.7889 (p) REVERT: E 23 SER cc_start: 0.8381 (t) cc_final: 0.7944 (p) REVERT: E 43 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7413 (mtpm) REVERT: E 85 SER cc_start: 0.8517 (m) cc_final: 0.8072 (p) REVERT: A 248 PHE cc_start: 0.7602 (t80) cc_final: 0.7309 (t80) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 1.3455 time to fit residues: 189.5582 Evaluate side-chains 141 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8953 Z= 0.169 Angle : 0.486 7.191 12142 Z= 0.260 Chirality : 0.040 0.135 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.190 22.105 1217 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.98 % Allowed : 15.74 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.60 (0.26), residues: 1098 helix: 2.63 (0.27), residues: 386 sheet: 0.61 (0.29), residues: 290 loop : -0.04 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.032 Fit side-chains REVERT: B 10 LYS cc_start: 0.7725 (mttt) cc_final: 0.7176 (mttt) REVERT: B 21 LYS cc_start: 0.7667 (tttm) cc_final: 0.7085 (ttpt) REVERT: B 24 ARG cc_start: 0.6595 (mtm-85) cc_final: 0.6280 (mtm-85) REVERT: B 132 ARG cc_start: 0.8308 (ptt-90) cc_final: 0.7995 (ptt-90) REVERT: B 195 LYS cc_start: 0.7341 (tttm) cc_final: 0.6980 (ttpp) REVERT: B 208 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6219 (mmm160) REVERT: B 222 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: B 232 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7844 (ttpt) REVERT: C 52 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7538 (mtt90) REVERT: C 217 MET cc_start: 0.8169 (pmm) cc_final: 0.7670 (pmm) REVERT: C 219 ARG cc_start: 0.7627 (mmm160) cc_final: 0.7301 (mtp180) REVERT: C 256 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7217 (mtp180) REVERT: D 21 MET cc_start: 0.6387 (mtm) cc_final: 0.5783 (tmt) REVERT: E 7 SER cc_start: 0.8196 (t) cc_final: 0.7958 (p) REVERT: E 23 SER cc_start: 0.8363 (t) cc_final: 0.7952 (p) REVERT: E 43 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7374 (mtpm) REVERT: E 85 SER cc_start: 0.8500 (m) cc_final: 0.8061 (p) outliers start: 28 outliers final: 24 residues processed: 132 average time/residue: 1.3679 time to fit residues: 191.3977 Evaluate side-chains 140 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8953 Z= 0.139 Angle : 0.472 6.894 12142 Z= 0.250 Chirality : 0.040 0.139 1388 Planarity : 0.004 0.046 1531 Dihedral : 3.981 21.101 1217 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.87 % Allowed : 15.96 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.73 (0.26), residues: 1098 helix: 2.71 (0.27), residues: 387 sheet: 0.70 (0.29), residues: 290 loop : 0.04 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.004 0.001 HIS A 103 PHE 0.014 0.001 PHE C 199 TYR 0.012 0.001 TYR E 178 ARG 0.008 0.000 ARG C 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.068 Fit side-chains REVERT: B 10 LYS cc_start: 0.7682 (mttt) cc_final: 0.7184 (mttt) REVERT: B 21 LYS cc_start: 0.7636 (tttm) cc_final: 0.7073 (ttpt) REVERT: B 24 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.6253 (mtm-85) REVERT: B 132 ARG cc_start: 0.8277 (ptt-90) cc_final: 0.7961 (ptt-90) REVERT: B 195 LYS cc_start: 0.7381 (tttm) cc_final: 0.7076 (ttpp) REVERT: B 208 ARG cc_start: 0.7075 (mtm110) cc_final: 0.6207 (mmm160) REVERT: B 222 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: B 232 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7851 (tttt) REVERT: C 52 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7543 (mtt90) REVERT: C 217 MET cc_start: 0.8210 (pmm) cc_final: 0.7812 (pmm) REVERT: C 219 ARG cc_start: 0.7577 (mmm160) cc_final: 0.7288 (mtp180) REVERT: C 256 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: D 21 MET cc_start: 0.6354 (mtm) cc_final: 0.5754 (tmt) REVERT: E 23 SER cc_start: 0.8375 (t) cc_final: 0.7975 (p) REVERT: E 43 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7362 (mtpt) REVERT: E 85 SER cc_start: 0.8498 (m) cc_final: 0.8064 (p) REVERT: A 330 MET cc_start: 0.7918 (ttp) cc_final: 0.7707 (ptm) outliers start: 27 outliers final: 18 residues processed: 132 average time/residue: 1.3607 time to fit residues: 190.5091 Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.180051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122229 restraints weight = 8597.943| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.62 r_work: 0.3179 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8953 Z= 0.194 Angle : 0.506 8.214 12142 Z= 0.269 Chirality : 0.041 0.137 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.182 21.986 1217 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.77 % Allowed : 15.85 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.67 (0.26), residues: 1098 helix: 2.67 (0.27), residues: 386 sheet: 0.65 (0.29), residues: 291 loop : 0.02 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE C 151 TYR 0.014 0.001 TYR B 212 ARG 0.009 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.38 seconds wall clock time: 72 minutes 15.50 seconds (4335.50 seconds total)