Starting phenix.real_space_refine on Sat Apr 6 01:31:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unv_42418/04_2024/8unv_42418_updated.pdb" } resolution = 3.3 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= 0.023 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 40 5.16 5 C 4229 2.51 5 N 1136 2.21 5 O 1183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6591 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1712 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 156 Conformer: "B" Number of residues, atoms: 233, 1712 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 156 bond proxies already assigned to first conformer: 1733 Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2383 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 164 Chain: "G" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 334 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2103 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 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: 5.15, per 1000 atoms: 0.78 Number of scatterers: 6591 At special positions: 0 Unit cell: (84.1669, 137.097, 98.0501, 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 40 16.00 P 3 15.00 O 1183 8.00 N 1136 7.00 C 4229 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=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 43.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.604A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.878A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.679A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.577A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.991A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 60 removed outlier: 3.524A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.737A pdb=" N PHE R 71 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL R 87 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.596A pdb=" N THR R 96 " --> pdb=" O HIS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.070A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.785A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 removed outlier: 3.589A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.604A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 4.031A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.838A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.561A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 4.144A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.418A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.085A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.960A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.092A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.920A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.836A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.961A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 897 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: 2.08 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1485 1.33 - 1.45: 1511 1.45 - 1.57: 3681 1.57 - 1.69: 5 1.69 - 1.81: 54 Bond restraints: 6736 Sorted by residual: bond pdb=" C VAL R 31 " pdb=" O VAL R 31 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.17e-02 7.31e+03 2.43e+01 bond pdb=" C GLY R 35 " pdb=" O GLY R 35 " ideal model delta sigma weight residual 1.234 1.279 -0.045 1.20e-02 6.94e+03 1.43e+01 bond pdb=" C ILE R 154 " pdb=" N LEU R 155 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" N VAL R 31 " pdb=" CA VAL R 31 " ideal model delta sigma weight residual 1.461 1.504 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.461 1.502 -0.042 1.19e-02 7.06e+03 1.24e+01 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.07: 157 107.07 - 113.84: 3812 113.84 - 120.60: 2771 120.60 - 127.36: 2413 127.36 - 134.13: 73 Bond angle restraints: 9226 Sorted by residual: angle pdb=" N TRP R 173 " pdb=" CA TRP R 173 " pdb=" C TRP R 173 " ideal model delta sigma weight residual 111.28 117.67 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" C ILE R 47 " pdb=" N VAL R 48 " pdb=" CA VAL R 48 " ideal model delta sigma weight residual 122.35 115.84 6.51 1.18e+00 7.18e-01 3.05e+01 angle pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" O GLY A 49 " ideal model delta sigma weight residual 121.41 116.66 4.75 8.80e-01 1.29e+00 2.92e+01 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 105.55 5.73 1.09e+00 8.42e-01 2.76e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 ... (remaining 9221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.34: 3777 31.34 - 62.69: 97 62.69 - 94.03: 7 94.03 - 125.37: 1 125.37 - 156.71: 2 Dihedral angle restraints: 3884 sinusoidal: 1223 harmonic: 2661 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 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 -134.02 -156.71 1 2.00e+01 2.50e-03 4.60e+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 -40.98 145.58 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 3881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 802 0.050 - 0.100: 187 0.100 - 0.150: 86 0.150 - 0.200: 22 0.200 - 0.250: 8 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA HIS R 172 " pdb=" N HIS R 172 " pdb=" C HIS R 172 " pdb=" CB HIS R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET R 171 " pdb=" N MET R 171 " pdb=" C MET R 171 " pdb=" CB MET R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1102 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 60 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C PRO G 60 " 0.047 2.00e-02 2.50e+03 pdb=" O PRO G 60 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE G 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 52 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C THR G 52 " -0.046 2.00e-02 2.50e+03 pdb=" O THR G 52 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO G 53 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO G 49 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.035 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 510 2.74 - 3.28: 6489 3.28 - 3.82: 10320 3.82 - 4.36: 11450 4.36 - 4.90: 20976 Nonbonded interactions: 49745 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.201 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.316 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.403 2.440 nonbonded pdb=" OG SER A 51 " pdb=" O1G GTP A 401 " model vdw 2.405 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.431 2.520 ... (remaining 49740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 7.690 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.058 6736 Z= 0.386 Angle : 0.866 11.820 9226 Z= 0.597 Chirality : 0.058 0.250 1105 Planarity : 0.004 0.062 1159 Dihedral : 14.497 156.713 2152 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.34 % Allowed : 1.69 % Favored : 97.97 % 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: 0.91 (0.29), residues: 900 helix: 1.84 (0.27), residues: 384 sheet: 0.53 (0.44), residues: 168 loop : -0.75 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.005 0.001 HIS R 178 PHE 0.021 0.001 PHE A 212 TYR 0.016 0.001 TYR R 174 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.971 Fit side-chains REVERT: A 211 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8213 (mtpt) REVERT: A 368 ASP cc_start: 0.7935 (t0) cc_final: 0.7299 (p0) REVERT: R 107 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7538 (mt-10) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.2701 time to fit residues: 36.8806 Evaluate side-chains 84 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.0000 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6736 Z= 0.311 Angle : 0.546 6.472 9226 Z= 0.299 Chirality : 0.043 0.136 1105 Planarity : 0.004 0.050 1159 Dihedral : 8.180 133.846 1000 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 10.85 % Favored : 87.97 % 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: 0.62 (0.28), residues: 900 helix: 1.59 (0.26), residues: 394 sheet: 0.33 (0.42), residues: 177 loop : -0.95 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.006 0.001 HIS R 178 PHE 0.016 0.002 PHE B 235 TYR 0.013 0.001 TYR R 174 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.737 Fit side-chains REVERT: A 211 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8045 (mtpt) REVERT: R 318 ASN cc_start: 0.9284 (t0) cc_final: 0.9002 (t0) outliers start: 7 outliers final: 6 residues processed: 89 average time/residue: 0.1953 time to fit residues: 23.2174 Evaluate side-chains 85 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6736 Z= 0.249 Angle : 0.507 7.180 9226 Z= 0.274 Chirality : 0.042 0.129 1105 Planarity : 0.004 0.043 1159 Dihedral : 7.411 124.842 998 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 12.88 % Favored : 85.25 % 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: 0.52 (0.28), residues: 900 helix: 1.64 (0.26), residues: 392 sheet: 0.15 (0.41), residues: 176 loop : -1.11 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 235 TYR 0.010 0.001 TYR R 174 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.025 Fit side-chains REVERT: A 211 LYS cc_start: 0.8400 (mtmm) cc_final: 0.7910 (mtpt) REVERT: B 234 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: R 318 ASN cc_start: 0.9301 (t0) cc_final: 0.9038 (t0) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.2021 time to fit residues: 23.4581 Evaluate side-chains 87 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6736 Z= 0.195 Angle : 0.469 6.704 9226 Z= 0.255 Chirality : 0.041 0.128 1105 Planarity : 0.003 0.041 1159 Dihedral : 6.884 115.793 998 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.53 % Allowed : 13.73 % Favored : 84.75 % 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: 0.57 (0.28), residues: 900 helix: 1.68 (0.27), residues: 394 sheet: 0.14 (0.41), residues: 175 loop : -1.07 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE B 235 TYR 0.008 0.001 TYR R 174 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.736 Fit side-chains REVERT: A 211 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7767 (mtpt) REVERT: B 234 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: R 174 TYR cc_start: 0.8583 (p90) cc_final: 0.8373 (p90) REVERT: R 318 ASN cc_start: 0.9294 (t0) cc_final: 0.9035 (t0) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.1930 time to fit residues: 22.5800 Evaluate side-chains 87 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6736 Z= 0.186 Angle : 0.468 6.445 9226 Z= 0.254 Chirality : 0.041 0.130 1105 Planarity : 0.004 0.045 1159 Dihedral : 6.353 106.202 998 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.03 % Allowed : 14.41 % Favored : 83.56 % 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: 0.53 (0.28), residues: 900 helix: 1.68 (0.27), residues: 391 sheet: 0.17 (0.40), residues: 174 loop : -1.14 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE B 235 TYR 0.009 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.757 Fit side-chains REVERT: A 211 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7846 (mtpt) REVERT: B 234 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: R 318 ASN cc_start: 0.9371 (t0) cc_final: 0.9111 (t0) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.1917 time to fit residues: 23.1678 Evaluate side-chains 90 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6736 Z= 0.226 Angle : 0.488 7.166 9226 Z= 0.264 Chirality : 0.041 0.133 1105 Planarity : 0.004 0.052 1159 Dihedral : 6.040 99.369 998 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 14.92 % Favored : 82.54 % 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: 0.47 (0.28), residues: 900 helix: 1.62 (0.26), residues: 398 sheet: 0.06 (0.40), residues: 175 loop : -1.17 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.012 0.001 PHE B 235 TYR 0.018 0.001 TYR R 174 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.786 Fit side-chains REVERT: A 211 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7801 (mtpt) REVERT: B 234 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: R 316 TYR cc_start: 0.8184 (m-80) cc_final: 0.7862 (m-10) REVERT: R 318 ASN cc_start: 0.9349 (t0) cc_final: 0.9093 (t0) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1941 time to fit residues: 23.7245 Evaluate side-chains 92 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6736 Z= 0.137 Angle : 0.447 6.349 9226 Z= 0.242 Chirality : 0.040 0.131 1105 Planarity : 0.003 0.053 1159 Dihedral : 5.600 91.873 998 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.20 % Allowed : 15.59 % Favored : 82.20 % 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: 0.70 (0.28), residues: 900 helix: 1.85 (0.27), residues: 397 sheet: 0.15 (0.40), residues: 175 loop : -1.08 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS R 93 PHE 0.009 0.001 PHE R 217 TYR 0.017 0.001 TYR R 174 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.847 Fit side-chains REVERT: A 211 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7803 (mtpt) REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: R 316 TYR cc_start: 0.8056 (m-80) cc_final: 0.7839 (m-10) REVERT: R 318 ASN cc_start: 0.9348 (t0) cc_final: 0.9114 (t0) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1875 time to fit residues: 25.4474 Evaluate side-chains 96 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0050 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6736 Z= 0.116 Angle : 0.430 6.435 9226 Z= 0.230 Chirality : 0.039 0.131 1105 Planarity : 0.003 0.052 1159 Dihedral : 5.200 87.068 998 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Rotamer: Outliers : 2.03 % Allowed : 16.44 % Favored : 81.53 % 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: 0.86 (0.29), residues: 900 helix: 2.03 (0.27), residues: 395 sheet: 0.18 (0.41), residues: 176 loop : -1.03 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.017 0.001 TYR R 174 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.568 Fit side-chains REVERT: A 211 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7886 (mtpt) REVERT: B 234 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: R 318 ASN cc_start: 0.9377 (t0) cc_final: 0.9137 (t0) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.1832 time to fit residues: 26.0336 Evaluate side-chains 99 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6736 Z= 0.143 Angle : 0.455 7.255 9226 Z= 0.243 Chirality : 0.040 0.128 1105 Planarity : 0.004 0.058 1159 Dihedral : 5.194 86.250 998 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Rotamer: Outliers : 2.37 % Allowed : 17.46 % Favored : 80.17 % 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: 0.83 (0.29), residues: 900 helix: 2.01 (0.27), residues: 396 sheet: 0.13 (0.41), residues: 170 loop : -1.01 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 173 HIS 0.003 0.001 HIS A 220 PHE 0.007 0.001 PHE B 199 TYR 0.020 0.001 TYR R 174 ARG 0.001 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.680 Fit side-chains REVERT: A 211 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7852 (mtpp) REVERT: B 234 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: R 318 ASN cc_start: 0.9362 (t0) cc_final: 0.9105 (t0) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.1697 time to fit residues: 22.3268 Evaluate side-chains 98 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6736 Z= 0.155 Angle : 0.468 8.807 9226 Z= 0.250 Chirality : 0.040 0.136 1105 Planarity : 0.004 0.061 1159 Dihedral : 5.177 85.300 998 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.66 % Rotamer: Outliers : 2.03 % Allowed : 18.47 % Favored : 79.49 % 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: 0.83 (0.28), residues: 900 helix: 1.99 (0.27), residues: 396 sheet: 0.16 (0.41), residues: 169 loop : -0.99 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 173 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE A 222 TYR 0.019 0.001 TYR R 174 ARG 0.001 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.748 Fit side-chains REVERT: A 211 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7794 (mmmt) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: R 318 ASN cc_start: 0.9327 (t0) cc_final: 0.9062 (t0) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.1876 time to fit residues: 24.2233 Evaluate side-chains 97 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098916 restraints weight = 40498.787| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 5.24 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6736 Z= 0.146 Angle : 0.467 7.628 9226 Z= 0.250 Chirality : 0.040 0.159 1105 Planarity : 0.004 0.061 1159 Dihedral : 5.108 83.773 998 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Rotamer: Outliers : 2.20 % Allowed : 18.31 % Favored : 79.49 % Cbeta Deviations : 0.12 % 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: 0.85 (0.29), residues: 900 helix: 2.02 (0.27), residues: 396 sheet: 0.14 (0.42), residues: 169 loop : -0.99 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 222 TYR 0.017 0.001 TYR R 174 ARG 0.001 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.36 seconds wall clock time: 32 minutes 53.58 seconds (1973.58 seconds total)