Starting phenix.real_space_refine on Sat Aug 3 03:10:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/08_2024/8unx_42420.cif" } resolution = 3.6 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= 0.020 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 43 5.16 5 C 4297 2.51 5 N 1155 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 309": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 175": "NH1" <-> "NH2" Residue "R GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1783 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 244, 1771 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 179 Conformer: "B" Number of residues, atoms: 244, 1771 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 179 bond proxies already assigned to first conformer: 1792 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2400 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 15, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 339 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2119 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.78, per 1000 atoms: 0.86 Number of scatterers: 6688 At special positions: 0 Unit cell: (85.0346, 134.493, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 3 15.00 O 1190 8.00 N 1155 7.00 C 4297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 47.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 removed outlier: 3.791A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.545A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.700A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.938A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.674A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.504A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.792A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.908A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.645A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 61 removed outlier: 3.518A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.758A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.555A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.723A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.768A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.879A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.031A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 removed outlier: 4.004A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.182A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.902A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.174A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.945A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.051A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.757A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.382A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1083 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: 1.74 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2153 1.34 - 1.46: 1611 1.46 - 1.59: 3005 1.59 - 1.71: 5 1.71 - 1.84: 60 Bond restraints: 6834 Sorted by residual: bond pdb=" CA SER A 51 " pdb=" CB SER A 51 " ideal model delta sigma weight residual 1.526 1.482 0.044 1.36e-02 5.41e+03 1.04e+01 bond pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.58e+00 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.22e+00 bond pdb=" N GLU A 259 " pdb=" CA GLU A 259 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.23e-02 6.61e+03 8.00e+00 ... (remaining 6829 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.84: 165 106.84 - 113.72: 3860 113.72 - 120.59: 2968 120.59 - 127.47: 2289 127.47 - 134.35: 77 Bond angle restraints: 9359 Sorted by residual: angle pdb=" C ASN B 132 " pdb=" CA ASN B 132 " pdb=" CB ASN B 132 " ideal model delta sigma weight residual 116.63 104.25 12.38 1.16e+00 7.43e-01 1.14e+02 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 104.48 6.80 1.09e+00 8.42e-01 3.89e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 104.91 6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N ARG G 13 " pdb=" CA ARG G 13 " pdb=" C ARG G 13 " ideal model delta sigma weight residual 111.28 104.97 6.31 1.09e+00 8.42e-01 3.35e+01 angle pdb=" CA ASN B 132 " pdb=" C ASN B 132 " pdb=" N VAL B 133 " ideal model delta sigma weight residual 119.63 115.23 4.40 8.10e-01 1.52e+00 2.95e+01 ... (remaining 9354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 3881 31.82 - 63.64: 61 63.64 - 95.46: 3 95.46 - 127.28: 0 127.28 - 159.10: 4 Dihedral angle restraints: 3949 sinusoidal: 1251 harmonic: 2698 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -131.63 -159.10 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.92 -152.84 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -43.86 148.46 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 3946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 796 0.047 - 0.094: 206 0.094 - 0.141: 78 0.141 - 0.188: 29 0.188 - 0.235: 13 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE R 334 " pdb=" N ILE R 334 " pdb=" C ILE R 334 " pdb=" CB ILE R 334 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1119 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 125 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASN B 125 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN B 125 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLY A 47 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 175 " 0.012 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG R 175 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG R 175 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 176 " 0.015 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 325 2.72 - 3.27: 6733 3.27 - 3.81: 10397 3.81 - 4.36: 11754 4.36 - 4.90: 21001 Nonbonded interactions: 50210 Sorted by model distance: nonbonded pdb=" O LEU R 339 " pdb=" CD1 LEU R 339 " model vdw 2.177 3.460 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.262 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.284 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.296 3.040 ... (remaining 50205 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=0.49 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: 2.080 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.450 Find NCS groups from input model: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.006 0.053 6834 Z= 0.404 Angle : 0.964 12.378 9359 Z= 0.666 Chirality : 0.057 0.235 1122 Planarity : 0.006 0.098 1176 Dihedral : 13.805 159.097 2193 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.27), residues: 914 helix: 2.15 (0.26), residues: 392 sheet: 1.12 (0.42), residues: 169 loop : -0.69 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.002 PHE A 222 TYR 0.020 0.001 TYR R 185 ARG 0.012 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.715 Fit side-chains REVERT: A 253 TYR cc_start: 0.8595 (p90) cc_final: 0.8341 (p90) REVERT: A 255 MET cc_start: 0.7332 (tpp) cc_final: 0.7016 (mmm) REVERT: A 308 ILE cc_start: 0.7204 (mm) cc_final: 0.6876 (mm) REVERT: B 125 ASN cc_start: 0.9072 (t0) cc_final: 0.8832 (t0) REVERT: R 191 CYS cc_start: 0.6374 (t) cc_final: 0.6135 (t) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1880 time to fit residues: 27.6625 Evaluate side-chains 86 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6834 Z= 0.185 Angle : 0.535 10.534 9359 Z= 0.288 Chirality : 0.041 0.138 1122 Planarity : 0.004 0.040 1176 Dihedral : 10.392 147.405 1014 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.01 % Allowed : 9.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.28), residues: 914 helix: 2.33 (0.26), residues: 411 sheet: 0.96 (0.41), residues: 177 loop : -0.69 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE A 222 TYR 0.008 0.001 TYR B 111 ARG 0.008 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8596 (p90) cc_final: 0.8285 (p90) REVERT: A 255 MET cc_start: 0.7199 (tpp) cc_final: 0.6970 (mmm) REVERT: A 308 ILE cc_start: 0.7301 (mm) cc_final: 0.6962 (mm) REVERT: B 325 MET cc_start: 0.8350 (mmt) cc_final: 0.8146 (mmt) REVERT: R 171 MET cc_start: 0.6902 (mmt) cc_final: 0.6613 (mmt) outliers start: 6 outliers final: 5 residues processed: 102 average time/residue: 0.1684 time to fit residues: 23.4435 Evaluate side-chains 91 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.0000 chunk 65 optimal weight: 0.0170 chunk 80 optimal weight: 0.6980 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6834 Z= 0.141 Angle : 0.480 8.625 9359 Z= 0.256 Chirality : 0.039 0.135 1122 Planarity : 0.003 0.035 1176 Dihedral : 9.529 144.666 1014 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.18 % Allowed : 10.76 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.28), residues: 914 helix: 2.47 (0.26), residues: 411 sheet: 0.81 (0.40), residues: 178 loop : -0.65 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.009 0.001 HIS R 93 PHE 0.014 0.001 PHE A 222 TYR 0.008 0.001 TYR A 339 ARG 0.008 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7512 (mtm) cc_final: 0.7193 (mtt) REVERT: A 253 TYR cc_start: 0.8648 (p90) cc_final: 0.8355 (p90) REVERT: A 255 MET cc_start: 0.7182 (tpp) cc_final: 0.6628 (mmm) REVERT: A 308 ILE cc_start: 0.7316 (mm) cc_final: 0.6976 (mm) REVERT: B 325 MET cc_start: 0.8347 (mmt) cc_final: 0.8140 (mmt) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.1885 time to fit residues: 25.5615 Evaluate side-chains 92 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 153 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.0020 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6834 Z= 0.164 Angle : 0.479 7.699 9359 Z= 0.256 Chirality : 0.039 0.134 1122 Planarity : 0.003 0.036 1176 Dihedral : 9.224 144.808 1014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.34 % Allowed : 12.94 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.28), residues: 914 helix: 2.64 (0.26), residues: 405 sheet: 0.75 (0.40), residues: 182 loop : -0.69 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.009 0.001 HIS R 93 PHE 0.010 0.001 PHE B 199 TYR 0.006 0.001 TYR R 185 ARG 0.008 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8677 (p90) cc_final: 0.8372 (p90) REVERT: A 255 MET cc_start: 0.7123 (tpp) cc_final: 0.6551 (mmm) REVERT: A 308 ILE cc_start: 0.7374 (mm) cc_final: 0.7059 (mm) REVERT: A 344 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8062 (tp30) outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 0.1730 time to fit residues: 23.8707 Evaluate side-chains 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6834 Z= 0.168 Angle : 0.477 6.927 9359 Z= 0.256 Chirality : 0.039 0.140 1122 Planarity : 0.003 0.043 1176 Dihedral : 8.851 144.381 1014 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.68 % Allowed : 14.45 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.28), residues: 914 helix: 2.66 (0.26), residues: 405 sheet: 0.53 (0.39), residues: 176 loop : -0.67 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.010 0.001 HIS R 93 PHE 0.010 0.001 PHE B 199 TYR 0.009 0.001 TYR B 111 ARG 0.009 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8706 (p90) cc_final: 0.8414 (p90) REVERT: A 255 MET cc_start: 0.7120 (tpp) cc_final: 0.6542 (mmm) REVERT: A 308 ILE cc_start: 0.7360 (mm) cc_final: 0.7045 (mm) REVERT: A 344 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8176 (tp30) REVERT: R 224 GLN cc_start: 0.7267 (mt0) cc_final: 0.7062 (tp40) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.1564 time to fit residues: 21.9748 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6834 Z= 0.154 Angle : 0.470 9.854 9359 Z= 0.254 Chirality : 0.039 0.144 1122 Planarity : 0.003 0.047 1176 Dihedral : 8.439 143.665 1014 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.68 % Allowed : 15.29 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.28), residues: 914 helix: 2.72 (0.26), residues: 405 sheet: 0.54 (0.39), residues: 173 loop : -0.67 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.011 0.001 HIS R 93 PHE 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR B 111 ARG 0.011 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8664 (p90) cc_final: 0.8343 (p90) REVERT: A 255 MET cc_start: 0.7084 (tpp) cc_final: 0.6609 (mmm) REVERT: A 308 ILE cc_start: 0.7310 (mm) cc_final: 0.7009 (mm) REVERT: A 344 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8216 (tp30) outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.1678 time to fit residues: 24.0255 Evaluate side-chains 98 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 0.0470 chunk 34 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6834 Z= 0.190 Angle : 0.482 9.772 9359 Z= 0.263 Chirality : 0.040 0.152 1122 Planarity : 0.003 0.050 1176 Dihedral : 8.332 143.044 1014 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.18 % Allowed : 16.64 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.28), residues: 914 helix: 2.81 (0.26), residues: 403 sheet: 0.50 (0.39), residues: 173 loop : -0.71 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.015 0.001 HIS R 93 PHE 0.013 0.001 PHE A 222 TYR 0.006 0.001 TYR A 311 ARG 0.011 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8693 (p90) cc_final: 0.8370 (p90) REVERT: A 255 MET cc_start: 0.6907 (tpp) cc_final: 0.6469 (mmm) REVERT: A 308 ILE cc_start: 0.7346 (mm) cc_final: 0.7052 (mm) REVERT: A 344 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8217 (tp30) REVERT: R 173 TRP cc_start: 0.7842 (m-10) cc_final: 0.7510 (m-10) outliers start: 7 outliers final: 6 residues processed: 99 average time/residue: 0.1535 time to fit residues: 21.3115 Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 16 optimal weight: 0.0870 chunk 55 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6834 Z= 0.127 Angle : 0.458 11.124 9359 Z= 0.247 Chirality : 0.038 0.150 1122 Planarity : 0.003 0.052 1176 Dihedral : 8.013 141.027 1014 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.84 % Allowed : 17.14 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.28), residues: 914 helix: 2.94 (0.26), residues: 397 sheet: 0.48 (0.39), residues: 168 loop : -0.69 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.013 0.001 HIS R 93 PHE 0.008 0.001 PHE B 199 TYR 0.007 0.001 TYR B 111 ARG 0.011 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8633 (p90) cc_final: 0.8354 (p90) REVERT: A 255 MET cc_start: 0.6859 (tpp) cc_final: 0.6323 (mmm) REVERT: A 308 ILE cc_start: 0.7297 (mm) cc_final: 0.7017 (mm) REVERT: A 344 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8274 (tp30) REVERT: R 173 TRP cc_start: 0.7851 (m-10) cc_final: 0.7574 (m-10) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.1628 time to fit residues: 23.4417 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6834 Z= 0.186 Angle : 0.487 10.428 9359 Z= 0.264 Chirality : 0.040 0.157 1122 Planarity : 0.003 0.054 1176 Dihedral : 8.020 140.625 1014 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.01 % Allowed : 17.82 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.28), residues: 914 helix: 2.88 (0.26), residues: 404 sheet: 0.46 (0.39), residues: 176 loop : -0.67 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.018 0.001 HIS R 93 PHE 0.020 0.001 PHE R 289 TYR 0.007 0.001 TYR A 311 ARG 0.014 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8681 (p90) cc_final: 0.8384 (p90) REVERT: A 255 MET cc_start: 0.6777 (tpp) cc_final: 0.6375 (mmm) REVERT: A 308 ILE cc_start: 0.7297 (mm) cc_final: 0.7018 (mm) REVERT: A 344 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8234 (tp30) REVERT: R 173 TRP cc_start: 0.7924 (m-10) cc_final: 0.7670 (m-10) outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.1771 time to fit residues: 22.9507 Evaluate side-chains 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6834 Z= 0.147 Angle : 0.477 9.387 9359 Z= 0.257 Chirality : 0.039 0.159 1122 Planarity : 0.003 0.055 1176 Dihedral : 7.971 142.025 1014 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.01 % Allowed : 17.48 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.28), residues: 914 helix: 2.86 (0.26), residues: 403 sheet: 0.44 (0.39), residues: 168 loop : -0.70 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.018 0.001 HIS R 93 PHE 0.021 0.001 PHE R 289 TYR 0.008 0.001 TYR B 111 ARG 0.013 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8673 (p90) cc_final: 0.8401 (p90) REVERT: A 255 MET cc_start: 0.6761 (tpp) cc_final: 0.6350 (mmm) REVERT: A 308 ILE cc_start: 0.7281 (mm) cc_final: 0.7017 (mm) REVERT: A 344 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8218 (tp30) REVERT: R 173 TRP cc_start: 0.7934 (m-10) cc_final: 0.7692 (m-10) outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 0.1835 time to fit residues: 23.7342 Evaluate side-chains 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095819 restraints weight = 36419.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100631 restraints weight = 12966.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105182 restraints weight = 6574.031| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6834 Z= 0.179 Angle : 0.488 7.329 9359 Z= 0.264 Chirality : 0.040 0.160 1122 Planarity : 0.003 0.053 1176 Dihedral : 7.976 148.201 1014 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.01 % Allowed : 17.98 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.28), residues: 914 helix: 2.90 (0.26), residues: 404 sheet: 0.35 (0.38), residues: 172 loop : -0.63 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.012 0.001 HIS R 93 PHE 0.018 0.001 PHE R 289 TYR 0.007 0.001 TYR R 199 ARG 0.013 0.001 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.20 seconds wall clock time: 29 minutes 54.18 seconds (1794.18 seconds total)