Starting phenix.real_space_refine on Tue Sep 24 18:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuv_43541/09_2024/8vuv_43541.cif" } resolution = 3.69 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 149 atoms to isotropic. 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 36 5.16 5 C 5449 2.51 5 N 1465 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2835 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 18, 'TRANS': 352} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1496 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1583 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2672 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 14, 'TRANS': 342} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 7.07, per 1000 atoms: 0.82 Number of scatterers: 8586 At special positions: 0 Unit cell: (102.72, 101.864, 145.52, 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 36 16.00 O 1636 8.00 N 1465 7.00 C 5449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 19 sheets defined 25.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.573A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.901A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.809A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.571A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.804A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 186 No H-bonds generated for 'chain 'H' and resid 184 through 186' Processing helix chain 'L' and resid 125 through 129 Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.874A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.656A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.994A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.887A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.644A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.649A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.983A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 264' Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.948A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.835A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 7.188A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194 removed outlier: 6.624A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.908A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 357 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.769A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.574A pdb=" N THR H 109 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN H 39 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE H 50 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 122 through 126 removed outlier: 3.866A pdb=" N PHE H 124 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 138 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY H 136 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP H 141 " --> pdb=" O TYR H 173 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR H 173 " --> pdb=" O ASP H 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 122 through 126 removed outlier: 3.866A pdb=" N PHE H 124 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 138 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY H 136 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP H 141 " --> pdb=" O TYR H 173 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR H 173 " --> pdb=" O ASP H 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 148 through 151 removed outlier: 4.293A pdb=" N TYR H 191 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.960A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.462A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.949A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 131 through 132 Processing sheet with id=AB6, first strand: chain 'L' and resid 147 through 152 Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.567A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 199 through 202 removed outlier: 6.799A pdb=" N PHE B 169 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLU B 201 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 171 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 257 through 258 removed outlier: 4.002A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 343 through 344 304 hydrogen bonds defined for protein. 834 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: 2.57 Time building geometry restraints manager: 2.67 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: 2802 1.34 - 1.46: 2078 1.46 - 1.58: 3844 1.58 - 1.70: 1 1.70 - 1.82: 59 Bond restraints: 8784 Sorted by residual: bond pdb=" CB PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.15e+00 bond pdb=" CB PRO L 40 " pdb=" CG PRO L 40 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" CB PRO A 98 " pdb=" CG PRO A 98 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.71e+00 bond pdb=" CB LYS H 140 " pdb=" CG LYS H 140 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CB MET A 155 " pdb=" CG MET A 155 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.87e-01 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 11827 2.22 - 4.43: 138 4.43 - 6.65: 16 6.65 - 8.86: 7 8.86 - 11.08: 3 Bond angle restraints: 11991 Sorted by residual: angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA GLU A 213 " pdb=" CB GLU A 213 " pdb=" CG GLU A 213 " ideal model delta sigma weight residual 114.10 122.61 -8.51 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CB LYS H 140 " pdb=" CG LYS H 140 " pdb=" CD LYS H 140 " ideal model delta sigma weight residual 111.30 120.34 -9.04 2.30e+00 1.89e-01 1.54e+01 angle pdb=" CA LYS H 140 " pdb=" CB LYS H 140 " pdb=" CG LYS H 140 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N PRO B 148 " pdb=" CD PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 103.20 97.93 5.27 1.50e+00 4.44e-01 1.23e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4455 17.81 - 35.62: 575 35.62 - 53.42: 142 53.42 - 71.23: 23 71.23 - 89.04: 13 Dihedral angle restraints: 5208 sinusoidal: 1860 harmonic: 3348 Sorted by residual: dihedral pdb=" CA VAL H 101 " pdb=" C VAL H 101 " pdb=" N PHE H 102 " pdb=" CA PHE H 102 " ideal model delta harmonic sigma weight residual 180.00 -143.87 -36.13 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 142.87 -49.87 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CA ASP A 345 " pdb=" C ASP A 345 " pdb=" N ARG A 346 " pdb=" CA ARG A 346 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 995 0.042 - 0.083: 268 0.083 - 0.124: 107 0.124 - 0.166: 10 0.166 - 0.207: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" C PRO A 98 " pdb=" CB PRO A 98 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 164 " pdb=" N ILE A 164 " pdb=" C ILE A 164 " pdb=" CB ILE A 164 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1378 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 97 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 98 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.046 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO L 40 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 176 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO B 177 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.029 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 302 2.71 - 3.26: 8155 3.26 - 3.80: 12886 3.80 - 4.35: 15119 4.35 - 4.90: 26761 Nonbonded interactions: 63223 Sorted by model distance: nonbonded pdb=" O VAL L 3 " pdb=" OG SER L 26 " model vdw 2.159 3.040 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH1 ARG B 92 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS B 137 " pdb=" O GLU B 354 " model vdw 2.250 3.120 nonbonded pdb=" NE2 GLN B 95 " pdb=" OE1 GLU B 316 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP A 130 " pdb=" OG SER A 132 " model vdw 2.260 3.040 ... (remaining 63218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 10.130 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.830 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.003 0.113 8784 Z= 0.210 Angle : 0.628 11.075 11991 Z= 0.322 Chirality : 0.044 0.207 1381 Planarity : 0.005 0.081 1539 Dihedral : 17.327 89.039 3036 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.69 % Favored : 92.13 % Rotamer: Outliers : 0.11 % Allowed : 33.94 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.24 (0.25), residues: 1144 helix: 0.80 (0.32), residues: 256 sheet: -0.49 (0.29), residues: 368 loop : -1.91 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 98 HIS 0.002 0.001 HIS A 280 PHE 0.020 0.001 PHE L 100 TYR 0.009 0.001 TYR H 94 ARG 0.010 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: L 92 ASN cc_start: 0.6900 (t0) cc_final: 0.6669 (t0) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2537 time to fit residues: 35.9516 Evaluate side-chains 94 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0270 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8784 Z= 0.186 Angle : 0.596 8.860 11991 Z= 0.310 Chirality : 0.044 0.205 1381 Planarity : 0.005 0.080 1539 Dihedral : 4.491 29.279 1237 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.69 % Favored : 92.13 % Rotamer: Outliers : 4.07 % Allowed : 29.86 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.16 (0.25), residues: 1144 helix: 0.77 (0.31), residues: 267 sheet: -0.45 (0.28), residues: 366 loop : -1.86 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.002 0.000 HIS A 293 PHE 0.010 0.001 PHE L 100 TYR 0.013 0.001 TYR A 261 ARG 0.008 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8353 (tt) REVERT: L 92 ASN cc_start: 0.7000 (t0) cc_final: 0.6773 (t0) outliers start: 36 outliers final: 17 residues processed: 128 average time/residue: 0.2000 time to fit residues: 35.5348 Evaluate side-chains 109 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 0.0010 chunk 103 optimal weight: 0.0470 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 8784 Z= 0.158 Angle : 0.555 8.755 11991 Z= 0.286 Chirality : 0.043 0.202 1381 Planarity : 0.004 0.080 1539 Dihedral : 4.222 25.578 1235 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.92 % Rotamer: Outliers : 4.86 % Allowed : 28.28 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.02 (0.25), residues: 1144 helix: 0.89 (0.32), residues: 268 sheet: -0.30 (0.29), residues: 361 loop : -1.81 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 285 HIS 0.002 0.000 HIS A 293 PHE 0.020 0.001 PHE L 100 TYR 0.014 0.001 TYR A 261 ARG 0.006 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.6880 (tpp) cc_final: 0.6556 (tpp) REVERT: A 213 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6266 (pm20) REVERT: A 358 ASN cc_start: 0.7766 (t0) cc_final: 0.7510 (t0) REVERT: L 92 ASN cc_start: 0.7006 (t0) cc_final: 0.6774 (t0) REVERT: B 158 LEU cc_start: 0.8397 (tt) cc_final: 0.8184 (tt) REVERT: B 358 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6760 (tpp) outliers start: 43 outliers final: 24 residues processed: 136 average time/residue: 0.2014 time to fit residues: 38.4860 Evaluate side-chains 122 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0170 chunk 77 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 54 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8784 Z= 0.284 Angle : 0.620 9.553 11991 Z= 0.319 Chirality : 0.045 0.204 1381 Planarity : 0.005 0.080 1539 Dihedral : 4.532 31.278 1235 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 6.33 % Allowed : 26.92 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.13 (0.25), residues: 1144 helix: 0.79 (0.31), residues: 266 sheet: -0.39 (0.29), residues: 367 loop : -1.85 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 33 HIS 0.004 0.001 HIS A 134 PHE 0.018 0.001 PHE L 100 TYR 0.017 0.001 TYR L 49 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 94 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7035 (tpp) cc_final: 0.6708 (tpp) REVERT: A 213 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: A 346 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8258 (tpt-90) REVERT: H 140 LYS cc_start: 0.4463 (tppt) cc_final: 0.4199 (tppt) REVERT: L 92 ASN cc_start: 0.7082 (t0) cc_final: 0.6859 (t0) REVERT: B 358 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6878 (tpp) REVERT: B 365 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6978 (pp) outliers start: 56 outliers final: 43 residues processed: 139 average time/residue: 0.2139 time to fit residues: 40.6801 Evaluate side-chains 139 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 92 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8784 Z= 0.207 Angle : 0.578 7.667 11991 Z= 0.297 Chirality : 0.044 0.202 1381 Planarity : 0.004 0.080 1539 Dihedral : 4.457 30.612 1235 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.52 % Favored : 92.31 % Rotamer: Outliers : 6.11 % Allowed : 27.38 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1144 helix: 0.78 (0.31), residues: 270 sheet: -0.37 (0.29), residues: 364 loop : -1.85 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.002 0.001 HIS A 146 PHE 0.013 0.001 PHE L 100 TYR 0.014 0.001 TYR A 261 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 97 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7949 (m90) REVERT: A 209 MET cc_start: 0.6970 (tpp) cc_final: 0.6665 (tpp) REVERT: A 213 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: L 92 ASN cc_start: 0.7051 (t0) cc_final: 0.6818 (t0) REVERT: B 358 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6817 (tpp) REVERT: B 365 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6875 (pp) outliers start: 54 outliers final: 38 residues processed: 140 average time/residue: 0.1905 time to fit residues: 37.4386 Evaluate side-chains 134 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 92 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8784 Z= 0.417 Angle : 0.702 7.998 11991 Z= 0.367 Chirality : 0.049 0.208 1381 Planarity : 0.005 0.079 1539 Dihedral : 5.083 38.318 1235 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.88 % Favored : 89.95 % Rotamer: Outliers : 6.90 % Allowed : 27.71 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.45 (0.24), residues: 1144 helix: 0.47 (0.31), residues: 264 sheet: -0.54 (0.29), residues: 365 loop : -2.05 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 33 HIS 0.007 0.001 HIS A 134 PHE 0.021 0.002 PHE H 102 TYR 0.020 0.002 TYR L 49 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 94 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7124 (tpp) cc_final: 0.6890 (tpp) REVERT: A 213 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: H 98 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7440 (tmm-80) REVERT: H 140 LYS cc_start: 0.4619 (tppt) cc_final: 0.4267 (tppt) REVERT: L 92 ASN cc_start: 0.7258 (t0) cc_final: 0.7032 (t0) REVERT: B 95 GLN cc_start: 0.7189 (mp10) cc_final: 0.6909 (mp10) REVERT: B 187 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8062 (mmt90) REVERT: B 358 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7058 (tpp) outliers start: 61 outliers final: 42 residues processed: 146 average time/residue: 0.2209 time to fit residues: 43.7496 Evaluate side-chains 137 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 92 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8784 Z= 0.199 Angle : 0.587 7.606 11991 Z= 0.304 Chirality : 0.044 0.205 1381 Planarity : 0.004 0.078 1539 Dihedral : 4.674 35.043 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.52 % Favored : 92.31 % Rotamer: Outliers : 5.66 % Allowed : 29.07 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 1144 helix: 0.65 (0.31), residues: 267 sheet: -0.44 (0.29), residues: 364 loop : -1.94 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.003 0.001 HIS A 293 PHE 0.019 0.001 PHE L 100 TYR 0.016 0.001 TYR A 261 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 92 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 209 MET cc_start: 0.7012 (tpp) cc_final: 0.6713 (tpp) REVERT: A 213 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: H 3 GLN cc_start: 0.7732 (mp10) cc_final: 0.7530 (mp10) REVERT: H 98 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6976 (tmm-80) REVERT: L 92 ASN cc_start: 0.7161 (t0) cc_final: 0.6933 (t0) REVERT: B 158 LEU cc_start: 0.8366 (tt) cc_final: 0.8158 (tt) REVERT: B 358 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.6906 (tpp) outliers start: 50 outliers final: 33 residues processed: 133 average time/residue: 0.2305 time to fit residues: 41.9457 Evaluate side-chains 127 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8784 Z= 0.294 Angle : 0.628 7.234 11991 Z= 0.327 Chirality : 0.046 0.207 1381 Planarity : 0.005 0.078 1539 Dihedral : 4.778 36.342 1235 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.92 % Favored : 90.91 % Rotamer: Outliers : 5.66 % Allowed : 29.52 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.25), residues: 1144 helix: 0.66 (0.31), residues: 265 sheet: -0.49 (0.29), residues: 364 loop : -1.99 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 33 HIS 0.004 0.001 HIS A 146 PHE 0.021 0.001 PHE L 100 TYR 0.016 0.002 TYR A 261 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 89 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 166 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 209 MET cc_start: 0.7087 (tpp) cc_final: 0.6784 (tpp) REVERT: A 213 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6496 (pm20) REVERT: H 3 GLN cc_start: 0.7782 (mp10) cc_final: 0.7577 (mp10) REVERT: H 98 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7232 (tmm-80) REVERT: L 92 ASN cc_start: 0.7274 (t0) cc_final: 0.7055 (t0) REVERT: B 358 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7037 (tpp) outliers start: 50 outliers final: 39 residues processed: 132 average time/residue: 0.2239 time to fit residues: 39.9424 Evaluate side-chains 131 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.0010 chunk 66 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 168 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8784 Z= 0.189 Angle : 0.586 8.904 11991 Z= 0.302 Chirality : 0.044 0.204 1381 Planarity : 0.004 0.077 1539 Dihedral : 4.562 33.320 1235 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.26 % Favored : 92.57 % Rotamer: Outliers : 5.54 % Allowed : 29.52 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.19 (0.25), residues: 1144 helix: 0.72 (0.31), residues: 268 sheet: -0.42 (0.29), residues: 364 loop : -1.90 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.002 0.000 HIS A 293 PHE 0.023 0.001 PHE L 100 TYR 0.017 0.001 TYR A 261 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 89 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7281 (mt) REVERT: A 166 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 209 MET cc_start: 0.7009 (tpp) cc_final: 0.6728 (tpp) REVERT: A 213 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: H 3 GLN cc_start: 0.7758 (mp10) cc_final: 0.7548 (mp10) REVERT: H 98 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6928 (tmm-80) REVERT: L 92 ASN cc_start: 0.7164 (t0) cc_final: 0.6943 (t0) REVERT: B 158 LEU cc_start: 0.8365 (tt) cc_final: 0.8130 (tt) REVERT: B 306 ASP cc_start: 0.7375 (t70) cc_final: 0.6971 (t0) REVERT: B 358 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6869 (tpp) outliers start: 49 outliers final: 39 residues processed: 131 average time/residue: 0.2244 time to fit residues: 40.0500 Evaluate side-chains 130 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 9 optimal weight: 0.0000 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 0.0020 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- 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: 0.7169 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8784 Z= 0.189 Angle : 0.586 8.343 11991 Z= 0.302 Chirality : 0.044 0.226 1381 Planarity : 0.004 0.076 1539 Dihedral : 4.440 30.579 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.87 % Rotamer: Outliers : 5.32 % Allowed : 30.09 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.16 (0.25), residues: 1144 helix: 0.73 (0.31), residues: 270 sheet: -0.45 (0.29), residues: 368 loop : -1.84 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.002 0.000 HIS A 293 PHE 0.027 0.001 PHE L 100 TYR 0.018 0.001 TYR A 261 ARG 0.007 0.000 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7151 (mt) REVERT: A 166 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8433 (tt) REVERT: A 209 MET cc_start: 0.7022 (tpp) cc_final: 0.6735 (tpp) REVERT: A 213 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: H 3 GLN cc_start: 0.7705 (mp10) cc_final: 0.7495 (mp10) REVERT: H 98 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6792 (tmm-80) REVERT: L 92 ASN cc_start: 0.7135 (t0) cc_final: 0.6911 (t0) REVERT: B 158 LEU cc_start: 0.8368 (tt) cc_final: 0.8129 (tt) REVERT: B 306 ASP cc_start: 0.7360 (t70) cc_final: 0.6999 (t0) REVERT: B 358 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6826 (tpp) outliers start: 47 outliers final: 38 residues processed: 131 average time/residue: 0.2058 time to fit residues: 37.2035 Evaluate side-chains 132 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.184424 restraints weight = 11643.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.179779 restraints weight = 22224.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.176891 restraints weight = 22353.118| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8784 Z= 0.304 Angle : 0.649 8.148 11991 Z= 0.337 Chirality : 0.047 0.272 1381 Planarity : 0.005 0.075 1539 Dihedral : 4.783 35.398 1235 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 5.20 % Allowed : 30.20 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.25), residues: 1144 helix: 0.63 (0.31), residues: 268 sheet: -0.57 (0.28), residues: 373 loop : -1.94 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 33 HIS 0.004 0.001 HIS A 162 PHE 0.024 0.002 PHE L 100 TYR 0.016 0.002 TYR A 261 ARG 0.006 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.04 seconds wall clock time: 37 minutes 13.79 seconds (2233.79 seconds total)