Starting phenix.real_space_refine on Fri Dec 8 15:34:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/12_2023/7wj5_32543.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.033 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 65 5.16 5 C 5551 2.51 5 N 1476 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.05, per 1000 atoms: 0.58 Number of scatterers: 8660 At special positions: 0 Unit cell: (106.112, 124.35, 117.718, 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 65 16.00 O 1568 8.00 N 1476 7.00 C 5551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " 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: 3.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 35.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.895A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.209A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.735A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.560A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.776A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.902A 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 'R' and resid 42 through 71 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.822A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 106 removed outlier: 4.283A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.055A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.658A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'R' and resid 251 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.891A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.569A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.791A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.270A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AB7, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.544A pdb=" N PHE S 7 " --> pdb=" O THR S 10 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 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: 2.56 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2743 1.34 - 1.46: 2191 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8846 Sorted by residual: bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.516 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.06e-01 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 7.01e-01 bond pdb=" CG1 ILE R 209 " pdb=" CD1 ILE R 209 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.79e-01 bond pdb=" C ILE A 264 " pdb=" N ILE A 265 " ideal model delta sigma weight residual 1.327 1.304 0.023 2.97e-02 1.13e+03 5.99e-01 ... (remaining 8841 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.07: 151 106.07 - 113.07: 4858 113.07 - 120.06: 3015 120.06 - 127.06: 3874 127.06 - 134.06: 96 Bond angle restraints: 11994 Sorted by residual: angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 115.83 -6.02 2.21e+00 2.05e-01 7.42e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" C ARG R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.91e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4868 16.60 - 33.19: 297 33.19 - 49.79: 47 49.79 - 66.38: 7 66.38 - 82.98: 1 Dihedral angle restraints: 5220 sinusoidal: 1953 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N THR A 321 " pdb=" CA THR A 321 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+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 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 844 0.032 - 0.064: 374 0.064 - 0.096: 112 0.096 - 0.127: 46 0.127 - 0.159: 6 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1379 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 287 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO R 288 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 108 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 109 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 344 2.72 - 3.26: 8665 3.26 - 3.81: 14372 3.81 - 4.35: 17028 4.35 - 4.90: 30051 Nonbonded interactions: 70460 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.173 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" O SER R 244 " model vdw 2.199 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.206 2.440 nonbonded pdb=" O LYS A 349 " pdb=" ND2 ASN R 318 " model vdw 2.244 2.520 ... (remaining 70455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.130 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: 4.060 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.780 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 0.035 8846 Z= 0.237 Angle : 0.546 8.958 11994 Z= 0.288 Chirality : 0.041 0.159 1382 Planarity : 0.003 0.031 1495 Dihedral : 10.788 82.979 3102 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 7.63 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.33 (0.30), residues: 283 loop : -0.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 107 PHE 0.012 0.001 PHE E 27 TYR 0.010 0.001 TYR R 211 ARG 0.002 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.2184 time to fit residues: 64.9354 Evaluate side-chains 185 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0792 time to fit residues: 3.1338 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8846 Z= 0.177 Angle : 0.537 8.020 11994 Z= 0.279 Chirality : 0.041 0.146 1382 Planarity : 0.004 0.031 1495 Dihedral : 4.112 28.238 1215 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 12.09 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.26), residues: 1111 helix: 2.24 (0.28), residues: 350 sheet: 0.37 (0.29), residues: 282 loop : -0.11 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 234 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 193 average time/residue: 0.2177 time to fit residues: 57.3402 Evaluate side-chains 179 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0839 time to fit residues: 3.0555 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 18 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8846 Z= 0.158 Angle : 0.517 7.518 11994 Z= 0.271 Chirality : 0.041 0.141 1382 Planarity : 0.003 0.030 1495 Dihedral : 4.031 27.012 1215 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 12.42 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 350 sheet: 0.46 (0.30), residues: 266 loop : -0.20 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 0.969 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 180 average time/residue: 0.2259 time to fit residues: 54.9895 Evaluate side-chains 168 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0784 time to fit residues: 2.5488 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 60 optimal weight: 0.0870 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8846 Z= 0.135 Angle : 0.495 7.205 11994 Z= 0.261 Chirality : 0.040 0.143 1382 Planarity : 0.003 0.030 1495 Dihedral : 3.898 25.266 1215 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 1.53 % Allowed : 14.27 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.26), residues: 1111 helix: 2.26 (0.28), residues: 349 sheet: 0.43 (0.29), residues: 266 loop : -0.20 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 197 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE A 189 TYR 0.012 0.001 TYR R 205 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.029 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 181 average time/residue: 0.2189 time to fit residues: 53.7753 Evaluate side-chains 173 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0925 time to fit residues: 2.1684 ------------------------------------------------------------------------------- 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: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8846 Z= 0.178 Angle : 0.525 7.438 11994 Z= 0.275 Chirality : 0.041 0.153 1382 Planarity : 0.003 0.029 1495 Dihedral : 3.973 21.911 1215 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 13.73 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.06 (0.26), residues: 1111 helix: 2.29 (0.28), residues: 342 sheet: 0.37 (0.30), residues: 266 loop : -0.17 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 179 average time/residue: 0.2372 time to fit residues: 56.5743 Evaluate side-chains 170 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0801 time to fit residues: 2.8443 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8846 Z= 0.231 Angle : 0.575 12.118 11994 Z= 0.294 Chirality : 0.042 0.162 1382 Planarity : 0.003 0.030 1495 Dihedral : 4.114 21.469 1215 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 1.74 % Allowed : 14.92 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1111 helix: 2.16 (0.28), residues: 341 sheet: 0.24 (0.29), residues: 277 loop : -0.14 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 211 HIS 0.002 0.001 HIS B 183 PHE 0.023 0.001 PHE A 267 TYR 0.009 0.001 TYR E 103 ARG 0.007 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.023 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 0.2280 time to fit residues: 54.1616 Evaluate side-chains 170 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0822 time to fit residues: 2.7576 ------------------------------------------------------------------------------- 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: 0.9980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8846 Z= 0.185 Angle : 0.550 10.871 11994 Z= 0.283 Chirality : 0.041 0.177 1382 Planarity : 0.003 0.030 1495 Dihedral : 4.034 23.040 1215 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 1.31 % Allowed : 15.69 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1111 helix: 2.13 (0.28), residues: 342 sheet: 0.23 (0.30), residues: 268 loop : -0.15 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.017 0.001 PHE A 267 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 0.919 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 174 average time/residue: 0.2417 time to fit residues: 55.9780 Evaluate side-chains 166 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0872 time to fit residues: 2.7112 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8846 Z= 0.272 Angle : 0.601 10.463 11994 Z= 0.310 Chirality : 0.043 0.174 1382 Planarity : 0.004 0.037 1495 Dihedral : 4.276 21.744 1215 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.98 % Allowed : 16.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1111 helix: 2.04 (0.28), residues: 342 sheet: 0.08 (0.30), residues: 279 loop : -0.13 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 197 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE A 267 TYR 0.010 0.001 TYR E 103 ARG 0.007 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 0.946 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 171 average time/residue: 0.2265 time to fit residues: 52.6608 Evaluate side-chains 164 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1033 time to fit residues: 1.6351 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 64 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: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8846 Z= 0.181 Angle : 0.553 11.287 11994 Z= 0.287 Chirality : 0.041 0.179 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.104 24.552 1215 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 0.54 % Allowed : 18.19 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1111 helix: 1.96 (0.28), residues: 349 sheet: 0.23 (0.30), residues: 266 loop : -0.17 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.014 0.001 PHE A 267 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.068 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 168 average time/residue: 0.2346 time to fit residues: 53.0713 Evaluate side-chains 168 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0824 time to fit residues: 2.1495 ------------------------------------------------------------------------------- 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: 0.5980 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8846 Z= 0.180 Angle : 0.557 11.403 11994 Z= 0.289 Chirality : 0.041 0.181 1382 Planarity : 0.003 0.047 1495 Dihedral : 4.068 23.783 1215 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 0.22 % Allowed : 18.63 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1111 helix: 1.97 (0.28), residues: 350 sheet: 0.24 (0.30), residues: 266 loop : -0.15 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 197 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE A 267 TYR 0.010 0.001 TYR E 178 ARG 0.009 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.041 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 172 average time/residue: 0.2333 time to fit residues: 54.4926 Evaluate side-chains 164 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0886 time to fit residues: 1.6393 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129811 restraints weight = 11341.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130411 restraints weight = 9493.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131729 restraints weight = 9184.485| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8846 Z= 0.216 Angle : 0.571 11.371 11994 Z= 0.297 Chirality : 0.042 0.178 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.147 22.752 1215 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.33 % Allowed : 18.52 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1111 helix: 1.94 (0.28), residues: 350 sheet: 0.13 (0.30), residues: 277 loop : -0.11 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 197 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.001 PHE A 223 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.52 seconds wall clock time: 36 minutes 4.12 seconds (2164.12 seconds total)