Starting phenix.real_space_refine on Fri Sep 11 16:15:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.cif Found real_map, /net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.map" model { file = "/net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25hs_80118/09_2026/25hs_80118.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6445 2.51 5 N 1762 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10022 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 762 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "E" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 718 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "A" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2741 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4198 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1575 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 185} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'AZR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 10022 At special positions: 0 Unit cell: (87.36, 118.44, 169.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1771 8.00 N 1762 7.00 C 6445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 428.0 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 53.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 12 through 51 Processing helix chain 'D' and resid 53 through 67 removed outlier: 3.935A pdb=" N THR D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 81 Processing helix chain 'E' and resid 8 through 26 removed outlier: 3.968A pdb=" N VAL E 12 " --> pdb=" O TRP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 66 removed outlier: 3.566A pdb=" N GLY E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.630A pdb=" N GLU E 73 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 74 " --> pdb=" O GLU E 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 55 through 76 removed outlier: 4.131A pdb=" N VAL A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.848A pdb=" N TRP A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 103 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 125 through 143 removed outlier: 4.357A pdb=" N ILE A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 173 removed outlier: 3.743A pdb=" N PHE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Proline residue: A 165 - end of helix removed outlier: 4.480A pdb=" N GLU A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 192 Processing helix chain 'A' and resid 198 through 218 removed outlier: 4.026A pdb=" N LEU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.541A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 296 through 314 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 359 through 380 removed outlier: 4.115A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 39 removed outlier: 3.661A pdb=" N ILE B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.576A pdb=" N MET B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.014A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.560A pdb=" N PHE B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.720A pdb=" N VAL B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 161 " --> pdb=" O GLY B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.671A pdb=" N LEU B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.708A pdb=" N MET B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 282' Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.912A pdb=" N VAL B 296 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.588A pdb=" N GLY B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.927A pdb=" N ILE B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 374 removed outlier: 4.414A pdb=" N ILE B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.798A pdb=" N THR B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.832A pdb=" N GLN B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 554 removed outlier: 4.371A pdb=" N ALA B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Proline residue: B 540 - end of helix Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.746A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 4.066A pdb=" N ALA C 104 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 105 " --> pdb=" O TYR C 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 111 through 121 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.530A pdb=" N TYR C 172 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 173 " --> pdb=" O ALA C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 173' Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 233 through 249 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing sheet with id=AA1, first strand: chain 'E' and resid 87 through 91 removed outlier: 3.593A pdb=" N LEU C 267 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU C 226 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C 226 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR C 221 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN C 228 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 219 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 177 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N MET C 211 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS C 179 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG C 150 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 164 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 118 removed outlier: 4.133A pdb=" N ILE A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.610A pdb=" N ARG B 54 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 129 removed outlier: 6.510A pdb=" N LEU B 125 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA B 84 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG B 127 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B 82 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 263 removed outlier: 6.373A pdb=" N ILE B 251 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET B 262 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 249 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 508 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.571A pdb=" N LEU B 340 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 430 through 431 removed outlier: 3.637A pdb=" N VAL B 446 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 84 removed outlier: 5.589A pdb=" N LYS C 80 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 140 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER C 82 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU C 142 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU C 84 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 144 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 139 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS C 127 " --> pdb=" O ASP C 143 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1467 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: 1.50 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1615 1.31 - 1.44: 2690 1.44 - 1.56: 5847 1.56 - 1.69: 1 1.69 - 1.82: 78 Bond restraints: 10231 Sorted by residual: bond pdb=" C25 AZR B 601 " pdb=" S8 AZR B 601 " ideal model delta sigma weight residual 1.724 1.514 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C26 AZR B 601 " pdb=" S8 AZR B 601 " ideal model delta sigma weight residual 1.745 1.544 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C24 AZR B 601 " pdb=" N15 AZR B 601 " ideal model delta sigma weight residual 1.371 1.564 -0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" C26 AZR B 601 " pdb=" N15 AZR B 601 " ideal model delta sigma weight residual 1.296 1.420 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C21 AZR B 601 " pdb=" N13 AZR B 601 " ideal model delta sigma weight residual 1.338 1.448 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 10226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 13844 4.63 - 9.25: 28 9.25 - 13.88: 4 13.88 - 18.50: 1 18.50 - 23.13: 1 Bond angle restraints: 13878 Sorted by residual: angle pdb=" O30 AZR B 601 " pdb=" C29 AZR B 601 " pdb=" O31 AZR B 601 " ideal model delta sigma weight residual 127.29 104.16 23.13 3.00e+00 1.11e-01 5.94e+01 angle pdb=" N SER B 294 " pdb=" CA SER B 294 " pdb=" C SER B 294 " ideal model delta sigma weight residual 110.80 124.15 -13.35 2.13e+00 2.20e-01 3.93e+01 angle pdb=" C25 AZR B 601 " pdb=" S8 AZR B 601 " pdb=" C26 AZR B 601 " ideal model delta sigma weight residual 89.16 107.38 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C23 AZR B 601 " pdb=" C29 AZR B 601 " pdb=" O31 AZR B 601 " ideal model delta sigma weight residual 114.95 127.97 -13.02 3.00e+00 1.11e-01 1.88e+01 angle pdb=" O32 AZR B 601 " pdb=" S17 AZR B 601 " pdb=" O34 AZR B 601 " ideal model delta sigma weight residual 113.24 101.19 12.05 3.00e+00 1.11e-01 1.61e+01 ... (remaining 13873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5392 17.65 - 35.31: 554 35.31 - 52.96: 94 52.96 - 70.61: 28 70.61 - 88.27: 13 Dihedral angle restraints: 6081 sinusoidal: 2427 harmonic: 3654 Sorted by residual: dihedral pdb=" N SER B 294 " pdb=" C SER B 294 " pdb=" CA SER B 294 " pdb=" CB SER B 294 " ideal model delta harmonic sigma weight residual 122.80 133.43 -10.63 0 2.50e+00 1.60e-01 1.81e+01 dihedral pdb=" C SER B 294 " pdb=" N SER B 294 " pdb=" CA SER B 294 " pdb=" CB SER B 294 " ideal model delta harmonic sigma weight residual -122.60 -133.21 10.61 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" CA VAL B 296 " pdb=" C VAL B 296 " pdb=" N LYS B 297 " pdb=" CA LYS B 297 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 6078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1564 0.158 - 0.316: 2 0.316 - 0.475: 0 0.475 - 0.633: 0 0.633 - 0.791: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" CA SER B 294 " pdb=" N SER B 294 " pdb=" C SER B 294 " pdb=" CB SER B 294 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CB THR C 165 " pdb=" CA THR C 165 " pdb=" OG1 THR C 165 " pdb=" CG2 THR C 165 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" C19 AZR B 601 " pdb=" C18 AZR B 601 " pdb=" C20 AZR B 601 " pdb=" N13 AZR B 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.61 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1564 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 319 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B 320 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 165 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " -0.010 2.00e-02 2.50e+03 1.00e-02 2.50e+00 pdb=" CG TRP A 116 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " 0.000 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 187 2.71 - 3.26: 9686 3.26 - 3.80: 15611 3.80 - 4.35: 18957 4.35 - 4.90: 32582 Nonbonded interactions: 77023 Sorted by model distance: nonbonded pdb=" OG SER A 262 " pdb=" OE2 GLU A 283 " model vdw 2.159 3.040 nonbonded pdb=" O GLN C 193 " pdb=" NE2 GLN C 197 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A 141 " pdb=" O GLY A 155 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLN B 228 " pdb=" OG1 THR B 263 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS D 7 " pdb=" OE2 GLU A 376 " model vdw 2.267 3.120 ... (remaining 77018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 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 : 0.005 0.210 10232 Z= 0.247 Angle : 0.666 23.129 13878 Z= 0.306 Chirality : 0.045 0.791 1567 Planarity : 0.004 0.050 1774 Dihedral : 15.008 88.267 3743 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1270 helix: 2.07 (0.22), residues: 607 sheet: 0.27 (0.50), residues: 118 loop : -1.36 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 177 TYR 0.013 0.001 TYR A 64 PHE 0.011 0.001 PHE B 15 TRP 0.027 0.001 TRP A 116 HIS 0.002 0.000 HIS B 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.25 (10231) covalent geometry : angle 0.66578 / 0.31 (13878) hydrogen bonds : bond 0.15237 / 10.23 ( 501) hydrogen bonds : angle 5.88846 / 4.25 ( 1467) Misc. bond : bond 0.02171 / 1.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: C 211 MET cc_start: 0.7509 (tmm) cc_final: 0.7188 (tmm) REVERT: C 260 ASP cc_start: 0.6411 (m-30) cc_final: 0.6095 (t0) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1059 time to fit residues: 18.5406 Evaluate side-chains 109 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS B 55 HIS B 85 ASN B 462 GLN B 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.141088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111126 restraints weight = 21171.921| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.29 r_work: 0.3414 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10232 Z= 0.178 Angle : 0.622 9.394 13878 Z= 0.307 Chirality : 0.044 0.166 1567 Planarity : 0.004 0.049 1774 Dihedral : 4.917 58.072 1424 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1270 helix: 1.73 (0.21), residues: 620 sheet: 0.19 (0.49), residues: 114 loop : -1.45 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 262 TYR 0.015 0.002 TYR A 64 PHE 0.019 0.002 PHE A 328 TRP 0.023 0.001 TRP A 116 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (10231) covalent geometry : angle 0.62181 / 0.31 (13878) hydrogen bonds : bond 0.04530 / 3.04 ( 501) hydrogen bonds : angle 4.70328 / 3.42 ( 1467) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.377 Fit side-chains REVERT: A 115 ARG cc_start: 0.7409 (ptp-170) cc_final: 0.6914 (ptp-170) REVERT: A 116 TRP cc_start: 0.7784 (m-90) cc_final: 0.7486 (m-90) REVERT: A 166 MET cc_start: 0.6752 (mmt) cc_final: 0.5948 (mmt) REVERT: B 272 ASN cc_start: 0.8650 (t0) cc_final: 0.8368 (t0) REVERT: B 360 ASP cc_start: 0.8288 (m-30) cc_final: 0.8075 (t70) REVERT: B 468 GLN cc_start: 0.6779 (mp10) cc_final: 0.6492 (mp10) REVERT: C 122 MET cc_start: -0.1660 (mmm) cc_final: -0.1912 (mmm) REVERT: C 197 GLN cc_start: 0.6696 (mm-40) cc_final: 0.5940 (mm-40) REVERT: C 211 MET cc_start: 0.7597 (tmm) cc_final: 0.7242 (tmm) REVERT: C 260 ASP cc_start: 0.6845 (m-30) cc_final: 0.6156 (t0) outliers start: 7 outliers final: 6 residues processed: 129 average time/residue: 0.1135 time to fit residues: 20.3519 Evaluate side-chains 117 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 189 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 HIS A 241 GLN B 55 HIS B 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.141392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.111093 restraints weight = 21104.131| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 4.13 r_work: 0.3431 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10232 Z= 0.126 Angle : 0.547 8.089 13878 Z= 0.273 Chirality : 0.041 0.135 1567 Planarity : 0.004 0.048 1774 Dihedral : 4.444 58.048 1423 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.45 % Allowed : 11.08 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1270 helix: 1.84 (0.21), residues: 616 sheet: 0.21 (0.49), residues: 114 loop : -1.45 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.011 0.001 TYR B 146 PHE 0.015 0.001 PHE D 5 TRP 0.020 0.001 TRP A 377 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10231) covalent geometry : angle 0.54742 / 0.27 (13878) hydrogen bonds : bond 0.04036 / 2.72 ( 501) hydrogen bonds : angle 4.44797 / 3.26 ( 1467) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.6573 (mmt) cc_final: 0.5803 (mmt) REVERT: B 272 ASN cc_start: 0.8634 (t0) cc_final: 0.8329 (t0) REVERT: B 360 ASP cc_start: 0.8293 (m-30) cc_final: 0.8082 (t70) REVERT: B 468 GLN cc_start: 0.6747 (mp10) cc_final: 0.6507 (mp10) REVERT: C 197 GLN cc_start: 0.6492 (mm-40) cc_final: 0.5813 (mm-40) REVERT: C 211 MET cc_start: 0.7595 (tmm) cc_final: 0.7362 (tmm) REVERT: C 260 ASP cc_start: 0.6846 (m-30) cc_final: 0.6191 (t0) outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.1171 time to fit residues: 19.1873 Evaluate side-chains 116 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 189 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 26 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 HIS B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107183 restraints weight = 21319.166| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.15 r_work: 0.3488 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10232 Z= 0.113 Angle : 0.524 7.988 13878 Z= 0.262 Chirality : 0.041 0.141 1567 Planarity : 0.004 0.049 1774 Dihedral : 4.309 59.098 1423 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 1.54 % Allowed : 13.49 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1270 helix: 1.87 (0.21), residues: 620 sheet: 0.26 (0.49), residues: 111 loop : -1.45 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.009 0.001 TYR B 146 PHE 0.012 0.001 PHE A 328 TRP 0.029 0.001 TRP A 116 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10231) covalent geometry : angle 0.52401 / 0.26 (13878) hydrogen bonds : bond 0.03690 / 2.49 ( 501) hydrogen bonds : angle 4.27790 / 3.14 ( 1467) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 116 TRP cc_start: 0.7706 (m-90) cc_final: 0.7311 (m-90) REVERT: A 154 MET cc_start: 0.5646 (ttm) cc_final: 0.5410 (ttp) REVERT: B 272 ASN cc_start: 0.8607 (t0) cc_final: 0.8301 (t0) REVERT: B 360 ASP cc_start: 0.8229 (m-30) cc_final: 0.7997 (t70) REVERT: B 468 GLN cc_start: 0.6753 (mp10) cc_final: 0.6496 (mp10) REVERT: C 146 LEU cc_start: 0.6893 (mt) cc_final: 0.6671 (pt) REVERT: C 165 THR cc_start: 0.5614 (OUTLIER) cc_final: 0.5277 (m) REVERT: C 197 GLN cc_start: 0.6414 (mm-40) cc_final: 0.5780 (mm-40) REVERT: C 211 MET cc_start: 0.7283 (tmm) cc_final: 0.7015 (tmm) REVERT: C 260 ASP cc_start: 0.6475 (m-30) cc_final: 0.5731 (t0) outliers start: 16 outliers final: 9 residues processed: 123 average time/residue: 0.1169 time to fit residues: 19.5977 Evaluate side-chains 115 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 GLN B 85 ASN B 117 ASN B 232 HIS B 265 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.137120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106396 restraints weight = 21290.387| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.87 r_work: 0.3364 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10232 Z= 0.269 Angle : 0.712 11.328 13878 Z= 0.357 Chirality : 0.048 0.203 1567 Planarity : 0.005 0.047 1774 Dihedral : 4.918 50.715 1423 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 2.31 % Allowed : 14.84 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1270 helix: 1.15 (0.21), residues: 611 sheet: 0.15 (0.49), residues: 112 loop : -1.66 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 153 TYR 0.021 0.002 TYR D 45 PHE 0.021 0.002 PHE B 299 TRP 0.032 0.002 TRP A 377 HIS 0.009 0.002 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.27 (10231) covalent geometry : angle 0.71240 / 0.36 (13878) hydrogen bonds : bond 0.05601 / 3.76 ( 501) hydrogen bonds : angle 4.63378 / 3.40 ( 1467) Misc. bond : bond 0.00160 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: E 35 ARG cc_start: 0.7290 (mpt180) cc_final: 0.6805 (mmt-90) REVERT: A 77 MET cc_start: 0.8415 (mmm) cc_final: 0.8154 (mtt) REVERT: A 116 TRP cc_start: 0.7906 (m-90) cc_final: 0.7512 (m-90) REVERT: A 154 MET cc_start: 0.5817 (ttm) cc_final: 0.5593 (ttp) REVERT: A 285 LEU cc_start: 0.8116 (mm) cc_final: 0.7905 (mp) REVERT: B 272 ASN cc_start: 0.8752 (t0) cc_final: 0.8476 (t0) REVERT: B 360 ASP cc_start: 0.8441 (m-30) cc_final: 0.8211 (t70) REVERT: B 468 GLN cc_start: 0.6951 (mp10) cc_final: 0.6628 (mp10) REVERT: B 480 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6113 (p-80) REVERT: C 118 GLN cc_start: 0.4725 (OUTLIER) cc_final: 0.4311 (pp30) REVERT: C 146 LEU cc_start: 0.6827 (mt) cc_final: 0.6622 (pt) REVERT: C 197 GLN cc_start: 0.6402 (mm-40) cc_final: 0.5721 (mm-40) REVERT: C 211 MET cc_start: 0.7644 (tmm) cc_final: 0.6989 (tmm) REVERT: C 260 ASP cc_start: 0.7057 (m-30) cc_final: 0.6724 (m-30) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.1116 time to fit residues: 19.2749 Evaluate side-chains 117 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 89 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 GLN B 117 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.139720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104687 restraints weight = 21281.530| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.05 r_work: 0.3459 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10232 Z= 0.118 Angle : 0.548 7.751 13878 Z= 0.275 Chirality : 0.041 0.147 1567 Planarity : 0.004 0.048 1774 Dihedral : 4.555 54.981 1423 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 1.83 % Allowed : 16.57 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1270 helix: 1.70 (0.21), residues: 607 sheet: 0.21 (0.50), residues: 113 loop : -1.63 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.009 0.001 TYR B 407 PHE 0.014 0.001 PHE A 328 TRP 0.024 0.001 TRP A 377 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10231) covalent geometry : angle 0.54778 / 0.28 (13878) hydrogen bonds : bond 0.03943 / 2.67 ( 501) hydrogen bonds : angle 4.28171 / 3.17 ( 1467) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 116 TRP cc_start: 0.7835 (m-90) cc_final: 0.7592 (m-90) REVERT: B 272 ASN cc_start: 0.8614 (t0) cc_final: 0.8320 (t0) REVERT: B 286 MET cc_start: 0.8497 (mtt) cc_final: 0.8235 (mtt) REVERT: B 360 ASP cc_start: 0.8305 (m-30) cc_final: 0.8017 (t70) REVERT: B 468 GLN cc_start: 0.6771 (mp10) cc_final: 0.6489 (mp10) REVERT: C 197 GLN cc_start: 0.6354 (mm-40) cc_final: 0.5715 (mm-40) REVERT: C 211 MET cc_start: 0.7435 (tmm) cc_final: 0.6764 (tmm) REVERT: C 260 ASP cc_start: 0.6464 (m-30) cc_final: 0.5708 (t0) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.1072 time to fit residues: 17.8335 Evaluate side-chains 115 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108903 restraints weight = 21283.991| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.59 r_work: 0.3446 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10232 Z= 0.121 Angle : 0.554 8.308 13878 Z= 0.275 Chirality : 0.041 0.170 1567 Planarity : 0.004 0.048 1774 Dihedral : 4.473 55.273 1423 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 2.12 % Allowed : 16.47 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1270 helix: 1.81 (0.21), residues: 607 sheet: 0.23 (0.49), residues: 113 loop : -1.59 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.011 0.001 TYR B 146 PHE 0.013 0.001 PHE A 328 TRP 0.024 0.001 TRP A 254 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10231) covalent geometry : angle 0.55430 / 0.28 (13878) hydrogen bonds : bond 0.03840 / 2.59 ( 501) hydrogen bonds : angle 4.20363 / 3.10 ( 1467) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: E 35 ARG cc_start: 0.7123 (mpt180) cc_final: 0.6768 (mmt-90) REVERT: B 272 ASN cc_start: 0.8684 (t0) cc_final: 0.8408 (t0) REVERT: B 360 ASP cc_start: 0.8352 (m-30) cc_final: 0.8137 (t70) REVERT: B 468 GLN cc_start: 0.6813 (mp10) cc_final: 0.6544 (mp10) REVERT: C 197 GLN cc_start: 0.6424 (mm-40) cc_final: 0.5782 (mm-40) REVERT: C 211 MET cc_start: 0.7630 (tmm) cc_final: 0.6945 (tmm) REVERT: C 260 ASP cc_start: 0.6823 (m-30) cc_final: 0.6236 (t0) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.1125 time to fit residues: 18.1097 Evaluate side-chains 117 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 0.0170 chunk 41 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 104 optimal weight: 0.0060 chunk 20 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 overall best weight: 0.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.141323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.111677 restraints weight = 21312.304| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.55 r_work: 0.3474 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10232 Z= 0.096 Angle : 0.521 8.179 13878 Z= 0.260 Chirality : 0.040 0.155 1567 Planarity : 0.004 0.049 1774 Dihedral : 4.325 58.204 1423 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 1.45 % Allowed : 17.44 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1270 helix: 1.99 (0.22), residues: 612 sheet: 0.34 (0.50), residues: 111 loop : -1.62 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.013 0.001 TYR A 268 PHE 0.013 0.001 PHE A 8 TRP 0.035 0.001 TRP A 116 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (10231) covalent geometry : angle 0.52115 / 0.26 (13878) hydrogen bonds : bond 0.03158 / 2.13 ( 501) hydrogen bonds : angle 4.07698 / 3.02 ( 1467) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: D 49 SER cc_start: 0.7583 (m) cc_final: 0.7315 (t) REVERT: E 35 ARG cc_start: 0.7024 (mpt180) cc_final: 0.6681 (mmt-90) REVERT: E 56 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7787 (tmt170) REVERT: A 116 TRP cc_start: 0.7836 (m-90) cc_final: 0.7534 (m-90) REVERT: A 166 MET cc_start: 0.6536 (mmt) cc_final: 0.6044 (mmt) REVERT: B 272 ASN cc_start: 0.8619 (t0) cc_final: 0.8318 (t0) REVERT: B 286 MET cc_start: 0.8485 (mtt) cc_final: 0.8252 (mtt) REVERT: B 468 GLN cc_start: 0.6680 (mp10) cc_final: 0.6428 (mp10) REVERT: C 197 GLN cc_start: 0.6442 (mm-40) cc_final: 0.5824 (mm-40) REVERT: C 211 MET cc_start: 0.7629 (tmm) cc_final: 0.6921 (tmm) REVERT: C 260 ASP cc_start: 0.6747 (m-30) cc_final: 0.6317 (t0) outliers start: 15 outliers final: 12 residues processed: 120 average time/residue: 0.1122 time to fit residues: 18.7695 Evaluate side-chains 117 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.138057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.107557 restraints weight = 21314.799| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.73 r_work: 0.3415 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10232 Z= 0.161 Angle : 0.593 9.067 13878 Z= 0.294 Chirality : 0.043 0.153 1567 Planarity : 0.004 0.047 1774 Dihedral : 4.503 53.623 1423 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 1.73 % Allowed : 17.05 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1270 helix: 1.77 (0.21), residues: 611 sheet: 0.27 (0.49), residues: 114 loop : -1.60 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 153 TYR 0.012 0.001 TYR B 407 PHE 0.016 0.002 PHE B 299 TRP 0.024 0.001 TRP A 377 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (10231) covalent geometry : angle 0.59333 / 0.29 (13878) hydrogen bonds : bond 0.04198 / 2.83 ( 501) hydrogen bonds : angle 4.19919 / 3.09 ( 1467) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: E 56 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7849 (tmt170) REVERT: A 116 TRP cc_start: 0.7883 (m-90) cc_final: 0.7627 (m-90) REVERT: B 272 ASN cc_start: 0.8698 (t0) cc_final: 0.8419 (t0) REVERT: B 286 MET cc_start: 0.8623 (mtt) cc_final: 0.8369 (mtt) REVERT: B 468 GLN cc_start: 0.6764 (mp10) cc_final: 0.6454 (mp10) REVERT: C 197 GLN cc_start: 0.6454 (mm-40) cc_final: 0.5825 (mm-40) REVERT: C 211 MET cc_start: 0.7634 (tmm) cc_final: 0.6986 (tmm) REVERT: C 260 ASP cc_start: 0.6822 (m-30) cc_final: 0.6267 (t0) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.1160 time to fit residues: 17.8405 Evaluate side-chains 118 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.108472 restraints weight = 21101.760| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.54 r_work: 0.3457 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10232 Z= 0.116 Angle : 0.552 8.303 13878 Z= 0.275 Chirality : 0.041 0.139 1567 Planarity : 0.004 0.048 1774 Dihedral : 4.441 54.501 1423 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 1.64 % Allowed : 17.24 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1270 helix: 1.92 (0.21), residues: 607 sheet: 0.30 (0.49), residues: 114 loop : -1.60 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.011 0.001 TYR B 146 PHE 0.015 0.001 PHE A 8 TRP 0.025 0.001 TRP A 116 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10231) covalent geometry : angle 0.55205 / 0.28 (13878) hydrogen bonds : bond 0.03702 / 2.50 ( 501) hydrogen bonds : angle 4.15262 / 3.06 ( 1467) Misc. bond : bond 0.00039 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: E 35 ARG cc_start: 0.7130 (mpt180) cc_final: 0.6761 (mmt-90) REVERT: E 56 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7816 (tmt170) REVERT: A 116 TRP cc_start: 0.7888 (m-90) cc_final: 0.7650 (m-90) REVERT: A 166 MET cc_start: 0.6487 (mmt) cc_final: 0.5997 (mmt) REVERT: B 272 ASN cc_start: 0.8672 (t0) cc_final: 0.8377 (t0) REVERT: B 286 MET cc_start: 0.8579 (mtt) cc_final: 0.8345 (mtt) REVERT: B 468 GLN cc_start: 0.6669 (mp10) cc_final: 0.6379 (mp10) REVERT: C 197 GLN cc_start: 0.6451 (mm-40) cc_final: 0.5832 (mm-40) REVERT: C 211 MET cc_start: 0.7589 (tmm) cc_final: 0.6906 (tmm) REVERT: C 260 ASP cc_start: 0.6739 (m-30) cc_final: 0.6227 (t0) outliers start: 17 outliers final: 13 residues processed: 113 average time/residue: 0.1129 time to fit residues: 17.6064 Evaluate side-chains 116 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 0.0370 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 109 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN B 105 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.139878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.105358 restraints weight = 21355.155| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.01 r_work: 0.3497 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10232 Z= 0.106 Angle : 0.542 8.298 13878 Z= 0.270 Chirality : 0.040 0.146 1567 Planarity : 0.004 0.048 1774 Dihedral : 4.368 55.705 1423 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 1.64 % Allowed : 17.24 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1270 helix: 2.00 (0.22), residues: 607 sheet: 0.31 (0.50), residues: 111 loop : -1.59 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 251 TYR 0.011 0.001 TYR B 146 PHE 0.015 0.001 PHE A 8 TRP 0.025 0.001 TRP A 116 HIS 0.002 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10231) covalent geometry : angle 0.54170 / 0.27 (13878) hydrogen bonds : bond 0.03432 / 2.32 ( 501) hydrogen bonds : angle 4.08307 / 3.01 ( 1467) Misc. bond : bond 0.00025 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3004.97 seconds wall clock time: 51 minutes 59.90 seconds (3119.90 seconds total)