Starting phenix.real_space_refine on Fri Dec 8 16:30:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/12_2023/8fmz_29301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/12_2023/8fmz_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_29301/12_2023/8fmz_29301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/12_2023/8fmz_29301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/12_2023/8fmz_29301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/12_2023/8fmz_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-1.21rc1-5172/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: 5.13, per 1000 atoms: 0.59 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: 3.36 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: 0.95 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: 2.97 Time building geometry restraints manager: 3.62 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: 0.730 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: 0.000 Extract box with map and model: 4.120 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.970 Find NCS groups from input model: 0.220 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.550 ------------------------------------------------------------------------------- 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 : 0.960 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 1.1563 time to fit residues: 255.6309 Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8953 Z= 0.247 Angle : 0.543 6.158 12142 Z= 0.296 Chirality : 0.043 0.129 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.450 22.929 1217 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.66 % Allowed : 11.38 % Favored : 85.96 % 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: 2.42 (0.26), residues: 389 sheet: 0.68 (0.28), residues: 305 loop : 0.05 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.005 0.001 HIS D 44 PHE 0.021 0.002 PHE C 151 TYR 0.013 0.002 TYR E 178 ARG 0.007 0.001 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 160 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.124 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 149 average time/residue: 1.4267 time to fit residues: 225.0493 Evaluate side-chains 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.5704 time to fit residues: 5.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN E 130 GLN E 182 ASN A 52 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8953 Z= 0.250 Angle : 0.535 7.787 12142 Z= 0.290 Chirality : 0.042 0.139 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.474 22.976 1217 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.30 % Allowed : 13.72 % Favored : 82.98 % 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: 1.55 (0.25), residues: 1098 helix: 2.51 (0.26), residues: 382 sheet: 0.59 (0.28), residues: 303 loop : 0.02 (0.31), residues: 413 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 0.018 0.002 PHE C 151 TYR 0.012 0.002 TYR E 178 ARG 0.007 0.001 ARG B 135 *********************** 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 158 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.999 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 144 average time/residue: 1.3282 time to fit residues: 203.1001 Evaluate side-chains 135 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 8 average time/residue: 0.7026 time to fit residues: 7.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7770 ------------------------------------------------------------------------------- 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8953 Z= 0.159 Angle : 0.475 6.042 12142 Z= 0.258 Chirality : 0.040 0.134 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.175 22.305 1217 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.62 % Allowed : 14.68 % Favored : 81.70 % 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: 2.62 (0.26), residues: 386 sheet: 0.72 (0.29), residues: 289 loop : 0.00 (0.31), residues: 423 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 0.014 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG B 135 *********************** 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 159 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.043 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 140 average time/residue: 1.3245 time to fit residues: 197.0020 Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.4233 time to fit residues: 5.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 8953 Z= 0.387 Angle : 0.614 6.219 12142 Z= 0.331 Chirality : 0.046 0.150 1388 Planarity : 0.005 0.052 1531 Dihedral : 4.853 23.567 1217 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.32 % Allowed : 14.15 % Favored : 80.53 % 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: 1.33 (0.25), residues: 1098 helix: 2.34 (0.26), residues: 381 sheet: 0.52 (0.29), residues: 294 loop : -0.14 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.005 0.001 HIS E 35 PHE 0.024 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.006 0.001 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 169 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 0.897 Fit side-chains outliers start: 50 outliers final: 28 residues processed: 149 average time/residue: 1.3484 time to fit residues: 212.8894 Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.4051 time to fit residues: 6.0974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3533 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= 0.144 Angle : 0.465 8.086 12142 Z= 0.252 Chirality : 0.040 0.136 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.152 21.832 1217 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.09 % Allowed : 15.96 % Favored : 80.96 % 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: 1.66 (0.26), residues: 1098 helix: 2.62 (0.27), residues: 387 sheet: 0.79 (0.29), residues: 285 loop : -0.07 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.006 0.001 HIS A 103 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 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 147 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.916 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 1.2703 time to fit residues: 182.9444 Evaluate side-chains 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.0844 time to fit residues: 2.0506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8953 Z= 0.249 Angle : 0.529 8.332 12142 Z= 0.284 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.452 22.954 1217 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 16.17 % Favored : 80.53 % 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: 1.54 (0.25), residues: 1098 helix: 2.54 (0.26), residues: 386 sheet: 0.61 (0.28), residues: 291 loop : -0.06 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.005 0.001 HIS E 35 PHE 0.019 0.002 PHE C 151 TYR 0.012 0.002 TYR B 212 ARG 0.007 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 141 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.992 Fit side-chains outliers start: 31 outliers final: 25 residues processed: 127 average time/residue: 1.3711 time to fit residues: 185.0684 Evaluate side-chains 133 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.2334 time to fit residues: 4.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8953 Z= 0.156 Angle : 0.478 7.548 12142 Z= 0.256 Chirality : 0.040 0.151 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.191 22.026 1217 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.98 % Allowed : 16.49 % Favored : 80.53 % 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: 1.66 (0.26), residues: 1098 helix: 2.62 (0.27), residues: 387 sheet: 0.64 (0.29), residues: 291 loop : 0.06 (0.31), residues: 420 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 0.014 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.008 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 138 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.991 Fit side-chains outliers start: 28 outliers final: 25 residues processed: 127 average time/residue: 1.3186 time to fit residues: 178.2562 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.6790 time to fit residues: 8.8297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8953 Z= 0.165 Angle : 0.480 7.425 12142 Z= 0.257 Chirality : 0.040 0.146 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.172 21.954 1217 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.13 % Allowed : 17.66 % Favored : 80.21 % 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: 1.70 (0.26), residues: 1098 helix: 2.67 (0.26), residues: 387 sheet: 0.66 (0.29), residues: 291 loop : 0.05 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE C 199 TYR 0.012 0.001 TYR E 178 ARG 0.009 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 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.975 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 125 average time/residue: 1.2523 time to fit residues: 166.8154 Evaluate side-chains 126 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1285 time to fit residues: 1.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3747 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= 0.147 Angle : 0.470 7.136 12142 Z= 0.251 Chirality : 0.040 0.148 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.062 21.432 1217 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.02 % Allowed : 17.77 % Favored : 80.21 % 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: 1.75 (0.26), residues: 1098 helix: 2.70 (0.26), residues: 387 sheet: 0.75 (0.29), residues: 288 loop : 0.06 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 74 TYR 0.012 0.001 TYR E 178 ARG 0.009 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 133 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.988 Fit side-chains outliers start: 19 outliers final: 17 residues processed: 130 average time/residue: 1.2643 time to fit residues: 175.5762 Evaluate side-chains 124 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0829 time to fit residues: 1.5572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.180729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122055 restraints weight = 8558.917| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.77 r_work: 0.3166 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3782 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= 0.217 Angle : 0.515 7.478 12142 Z= 0.274 Chirality : 0.041 0.156 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.334 22.339 1217 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.34 % Allowed : 17.77 % Favored : 79.89 % 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: 1.64 (0.26), residues: 1098 helix: 2.60 (0.26), residues: 386 sheet: 0.67 (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 0.005 0.001 HIS E 35 PHE 0.017 0.001 PHE C 151 TYR 0.015 0.002 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: 3909.50 seconds wall clock time: 70 minutes 5.29 seconds (4205.29 seconds total)