Starting phenix.real_space_refine on Fri Aug 22 21:24:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286.map" model { file = "/net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flt_29286/08_2025/8flt_29286_neut.cif" } resolution = 3.03 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= -0.002 sd= 0.101 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 49 5.16 5 C 5154 2.51 5 N 1404 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8086 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1874 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2574 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 396 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'AIB:plan-1': 2, 'HRG:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2174 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 8086 At special positions: 0 Unit cell: (81.6, 96.9, 130.9, 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 49 16.00 O 1479 8.00 N 1404 7.00 C 5154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 323.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 44.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.596A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.618A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.548A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.339A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.674A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.703A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.505A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.502A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'R' and resid 178 through 212 Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.797A pdb=" N SER R 246 " --> pdb=" O ALA R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.735A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.807A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 424 removed outlier: 3.560A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.273A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.604A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.556A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.563A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.216A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.048A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.015A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.977A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.692A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.548A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1293 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: 1.32 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1305 1.32 - 1.44: 2356 1.44 - 1.56: 4529 1.56 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8260 Sorted by residual: bond pdb=" CZ HRG P 11 " pdb=" NH1 HRG P 11 " ideal model delta sigma weight residual 1.282 1.435 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" NE HRG P 11 " pdb=" CZ HRG P 11 " ideal model delta sigma weight residual 1.371 1.451 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CZ HRG P 11 " pdb=" NH2 HRG P 11 " ideal model delta sigma weight residual 1.380 1.311 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.36e-02 5.41e+03 1.03e+01 bond pdb=" CA ALA N 101 " pdb=" CB ALA N 101 " ideal model delta sigma weight residual 1.536 1.493 0.043 1.48e-02 4.57e+03 8.52e+00 ... (remaining 8255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10866 1.64 - 3.28: 273 3.28 - 4.92: 44 4.92 - 6.57: 17 6.57 - 8.21: 4 Bond angle restraints: 11204 Sorted by residual: angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" CB PRO N 100 " ideal model delta sigma weight residual 103.19 98.21 4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CA PHE N 108 " pdb=" CB PHE N 108 " pdb=" CG PHE N 108 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" C ILE R 190 " pdb=" N TYR R 191 " pdb=" CA TYR R 191 " ideal model delta sigma weight residual 121.14 114.06 7.08 1.75e+00 3.27e-01 1.64e+01 angle pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" C VAL A 224 " ideal model delta sigma weight residual 106.55 111.71 -5.16 1.45e+00 4.76e-01 1.26e+01 angle pdb=" CA ASN N 35 " pdb=" C ASN N 35 " pdb=" O ASN N 35 " ideal model delta sigma weight residual 120.99 117.02 3.97 1.12e+00 7.97e-01 1.26e+01 ... (remaining 11199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4436 17.86 - 35.73: 331 35.73 - 53.59: 65 53.59 - 71.45: 14 71.45 - 89.32: 5 Dihedral angle restraints: 4851 sinusoidal: 1859 harmonic: 2992 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 4848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 963 0.049 - 0.097: 244 0.097 - 0.146: 43 0.146 - 0.195: 6 0.195 - 0.244: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA ASN N 35 " pdb=" N ASN N 35 " pdb=" C ASN N 35 " pdb=" CB ASN N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1254 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 35 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C ASN N 35 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN N 35 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP N 36 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 105 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ARG N 105 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG N 105 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP N 106 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 31 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ASN N 31 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN N 31 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR N 32 " 0.013 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 534 2.74 - 3.28: 8260 3.28 - 3.82: 13888 3.82 - 4.36: 17350 4.36 - 4.90: 29676 Nonbonded interactions: 69708 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.194 3.040 nonbonded pdb=" N AIB P 1 " pdb=" O THR R 427 " model vdw 2.222 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.242 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.257 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.267 3.120 ... (remaining 69703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.840 Find NCS groups from input model: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 8263 Z= 0.226 Angle : 0.667 8.208 11210 Z= 0.399 Chirality : 0.044 0.244 1257 Planarity : 0.004 0.049 1422 Dihedral : 13.483 89.317 2910 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.12 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.27), residues: 1005 helix: 1.84 (0.27), residues: 399 sheet: -0.56 (0.33), residues: 217 loop : -0.33 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.012 0.002 TYR B 59 PHE 0.026 0.002 PHE R 335 TRP 0.018 0.002 TRP R 298 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8260) covalent geometry : angle 0.66582 (11204) SS BOND : bond 0.00206 ( 3) SS BOND : angle 1.67729 ( 6) hydrogen bonds : bond 0.14119 ( 454) hydrogen bonds : angle 6.35044 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.261 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.0965 time to fit residues: 16.2443 Evaluate side-chains 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN R 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133898 restraints weight = 9078.617| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.35 r_work: 0.3287 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8263 Z= 0.140 Angle : 0.524 5.533 11210 Z= 0.293 Chirality : 0.042 0.181 1257 Planarity : 0.004 0.040 1422 Dihedral : 5.245 57.733 1128 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.71 % Allowed : 5.19 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.09 (0.27), residues: 1005 helix: 2.43 (0.26), residues: 397 sheet: -0.57 (0.33), residues: 219 loop : -0.22 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.023 0.001 TYR R 191 PHE 0.030 0.002 PHE R 335 TRP 0.015 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8260) covalent geometry : angle 0.52223 (11204) SS BOND : bond 0.00166 ( 3) SS BOND : angle 1.88044 ( 6) hydrogen bonds : bond 0.04553 ( 454) hydrogen bonds : angle 4.76455 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.226 Fit side-chains REVERT: B 138 GLU cc_start: 0.7333 (tt0) cc_final: 0.6955 (pm20) REVERT: R 445 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6663 (mmt) outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.0971 time to fit residues: 15.8446 Evaluate side-chains 120 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 387 HIS B 110 ASN R 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.157725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132723 restraints weight = 8946.656| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.43 r_work: 0.3262 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8263 Z= 0.161 Angle : 0.534 5.518 11210 Z= 0.296 Chirality : 0.043 0.182 1257 Planarity : 0.004 0.041 1422 Dihedral : 5.232 58.635 1128 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.53 % Allowed : 6.85 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.04 (0.27), residues: 1005 helix: 2.37 (0.26), residues: 394 sheet: -0.56 (0.33), residues: 219 loop : -0.23 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.016 0.002 TRP R 298 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8260) covalent geometry : angle 0.53249 (11204) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.95859 ( 6) hydrogen bonds : bond 0.04476 ( 454) hydrogen bonds : angle 4.69308 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.260 Fit side-chains REVERT: B 135 VAL cc_start: 0.7703 (t) cc_final: 0.7371 (p) REVERT: B 138 GLU cc_start: 0.7459 (tt0) cc_final: 0.7026 (pm20) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.0973 time to fit residues: 16.2577 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.134963 restraints weight = 9098.568| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.38 r_work: 0.3298 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8263 Z= 0.132 Angle : 0.502 5.599 11210 Z= 0.279 Chirality : 0.042 0.176 1257 Planarity : 0.004 0.047 1422 Dihedral : 5.068 59.332 1128 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 8.15 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.18 (0.27), residues: 1005 helix: 2.52 (0.26), residues: 395 sheet: -0.51 (0.33), residues: 219 loop : -0.18 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8260) covalent geometry : angle 0.50078 (11204) SS BOND : bond 0.00090 ( 3) SS BOND : angle 1.72298 ( 6) hydrogen bonds : bond 0.04184 ( 454) hydrogen bonds : angle 4.54328 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.209 Fit side-chains REVERT: A 374 ARG cc_start: 0.6503 (ttm170) cc_final: 0.5874 (ttm110) REVERT: B 135 VAL cc_start: 0.7637 (t) cc_final: 0.7372 (p) REVERT: B 138 GLU cc_start: 0.7443 (tt0) cc_final: 0.6962 (pm20) REVERT: N 95 TYR cc_start: 0.7824 (m-80) cc_final: 0.7505 (m-80) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.0959 time to fit residues: 16.4377 Evaluate side-chains 128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.159390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.132708 restraints weight = 9099.926| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.42 r_work: 0.3278 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8263 Z= 0.137 Angle : 0.508 5.460 11210 Z= 0.281 Chirality : 0.042 0.177 1257 Planarity : 0.003 0.042 1422 Dihedral : 5.039 59.744 1128 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.65 % Allowed : 8.74 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.19 (0.27), residues: 1005 helix: 2.54 (0.26), residues: 395 sheet: -0.49 (0.33), residues: 219 loop : -0.20 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.024 0.001 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8260) covalent geometry : angle 0.50607 (11204) SS BOND : bond 0.00353 ( 3) SS BOND : angle 2.09970 ( 6) hydrogen bonds : bond 0.04188 ( 454) hydrogen bonds : angle 4.50730 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.272 Fit side-chains REVERT: A 374 ARG cc_start: 0.6682 (ttm170) cc_final: 0.6234 (ttm-80) REVERT: A 378 ASP cc_start: 0.7156 (m-30) cc_final: 0.6900 (m-30) REVERT: B 135 VAL cc_start: 0.7763 (t) cc_final: 0.7476 (p) REVERT: N 19 ARG cc_start: 0.7617 (tpt-90) cc_final: 0.7401 (ttt90) REVERT: N 95 TYR cc_start: 0.7841 (m-80) cc_final: 0.7558 (m-80) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.0999 time to fit residues: 17.0461 Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 25 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.160693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.136758 restraints weight = 8968.058| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.34 r_work: 0.3315 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8263 Z= 0.113 Angle : 0.475 5.489 11210 Z= 0.265 Chirality : 0.041 0.172 1257 Planarity : 0.003 0.041 1422 Dihedral : 4.864 59.138 1128 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.30 % Allowed : 9.80 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.50 (0.27), residues: 1005 helix: 2.93 (0.26), residues: 383 sheet: -0.46 (0.33), residues: 219 loop : 0.01 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.024 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8260) covalent geometry : angle 0.47430 (11204) SS BOND : bond 0.00343 ( 3) SS BOND : angle 1.44935 ( 6) hydrogen bonds : bond 0.03980 ( 454) hydrogen bonds : angle 4.42860 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.296 Fit side-chains REVERT: A 374 ARG cc_start: 0.6583 (ttm170) cc_final: 0.6168 (ttm-80) REVERT: A 378 ASP cc_start: 0.7084 (m-30) cc_final: 0.6819 (m-30) REVERT: B 135 VAL cc_start: 0.7734 (t) cc_final: 0.7517 (p) REVERT: B 197 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7711 (mmm160) REVERT: N 20 LEU cc_start: 0.7632 (mt) cc_final: 0.7359 (mt) outliers start: 11 outliers final: 9 residues processed: 129 average time/residue: 0.0896 time to fit residues: 15.3276 Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN B 75 GLN ** B 340 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 = 0.3696 r_free = 0.3696 target = 0.160296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.133688 restraints weight = 9138.167| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.42 r_work: 0.3296 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8263 Z= 0.121 Angle : 0.485 5.545 11210 Z= 0.270 Chirality : 0.041 0.173 1257 Planarity : 0.003 0.041 1422 Dihedral : 4.839 58.581 1128 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.65 % Allowed : 10.04 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.47 (0.27), residues: 1005 helix: 2.93 (0.26), residues: 383 sheet: -0.54 (0.33), residues: 223 loop : 0.02 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.024 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8260) covalent geometry : angle 0.48330 (11204) SS BOND : bond 0.00231 ( 3) SS BOND : angle 1.55762 ( 6) hydrogen bonds : bond 0.03996 ( 454) hydrogen bonds : angle 4.40371 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.318 Fit side-chains REVERT: A 374 ARG cc_start: 0.6632 (ttm170) cc_final: 0.6175 (ttm-80) REVERT: A 378 ASP cc_start: 0.6983 (m-30) cc_final: 0.6759 (m-30) REVERT: A 392 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6511 (mt-10) REVERT: B 44 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8230 (mm-40) REVERT: B 197 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7734 (mmm160) REVERT: N 20 LEU cc_start: 0.7697 (mt) cc_final: 0.7393 (mt) outliers start: 14 outliers final: 12 residues processed: 130 average time/residue: 0.0934 time to fit residues: 15.9890 Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.162400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138642 restraints weight = 8992.063| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.36 r_work: 0.3337 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8263 Z= 0.102 Angle : 0.467 5.999 11210 Z= 0.261 Chirality : 0.040 0.169 1257 Planarity : 0.003 0.043 1422 Dihedral : 4.685 57.966 1128 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 10.98 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.64 (0.27), residues: 1005 helix: 3.05 (0.26), residues: 383 sheet: -0.39 (0.34), residues: 210 loop : 0.06 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.024 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8260) covalent geometry : angle 0.46599 (11204) SS BOND : bond 0.00192 ( 3) SS BOND : angle 1.21962 ( 6) hydrogen bonds : bond 0.03811 ( 454) hydrogen bonds : angle 4.29440 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.236 Fit side-chains REVERT: A 374 ARG cc_start: 0.6469 (ttm170) cc_final: 0.6030 (ttm-80) REVERT: A 378 ASP cc_start: 0.6954 (m-30) cc_final: 0.6676 (m-30) REVERT: A 392 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6433 (mt-10) REVERT: B 44 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 197 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7690 (mmm160) REVERT: N 20 LEU cc_start: 0.7588 (mt) cc_final: 0.7311 (mt) outliers start: 9 outliers final: 8 residues processed: 128 average time/residue: 0.0941 time to fit residues: 15.7416 Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133035 restraints weight = 9054.453| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.41 r_work: 0.3293 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8263 Z= 0.134 Angle : 0.504 9.183 11210 Z= 0.279 Chirality : 0.042 0.175 1257 Planarity : 0.003 0.042 1422 Dihedral : 4.795 57.391 1128 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 10.98 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.27), residues: 1005 helix: 2.92 (0.26), residues: 383 sheet: -0.50 (0.33), residues: 223 loop : 0.08 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.023 0.001 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8260) covalent geometry : angle 0.50307 (11204) SS BOND : bond 0.00241 ( 3) SS BOND : angle 1.40827 ( 6) hydrogen bonds : bond 0.04045 ( 454) hydrogen bonds : angle 4.37623 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 374 ARG cc_start: 0.6648 (ttm170) cc_final: 0.6186 (ttm-80) REVERT: A 378 ASP cc_start: 0.7026 (m-30) cc_final: 0.6759 (m-30) REVERT: A 392 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6524 (mt-10) REVERT: B 44 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8221 (mm-40) REVERT: N 20 LEU cc_start: 0.7674 (mt) cc_final: 0.7303 (mt) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.1174 time to fit residues: 19.7702 Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136953 restraints weight = 8952.441| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.35 r_work: 0.3313 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8263 Z= 0.120 Angle : 0.505 12.590 11210 Z= 0.278 Chirality : 0.041 0.172 1257 Planarity : 0.003 0.043 1422 Dihedral : 4.787 57.533 1128 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.30 % Allowed : 11.33 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.56 (0.27), residues: 1005 helix: 2.94 (0.25), residues: 383 sheet: -0.38 (0.34), residues: 210 loop : 0.03 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.023 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8260) covalent geometry : angle 0.50392 (11204) SS BOND : bond 0.00214 ( 3) SS BOND : angle 1.26973 ( 6) hydrogen bonds : bond 0.03964 ( 454) hydrogen bonds : angle 4.35809 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 374 ARG cc_start: 0.6548 (ttm170) cc_final: 0.6135 (ttm-80) REVERT: A 378 ASP cc_start: 0.6996 (m-30) cc_final: 0.6741 (m-30) REVERT: A 392 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6443 (mt-10) REVERT: B 44 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8199 (mm-40) outliers start: 11 outliers final: 10 residues processed: 128 average time/residue: 0.1118 time to fit residues: 18.5123 Evaluate side-chains 131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.159192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131805 restraints weight = 9006.764| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.46 r_work: 0.3276 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8263 Z= 0.131 Angle : 0.521 14.113 11210 Z= 0.286 Chirality : 0.042 0.176 1257 Planarity : 0.003 0.042 1422 Dihedral : 4.839 57.781 1128 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.53 % Allowed : 11.45 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.27), residues: 1005 helix: 2.87 (0.25), residues: 383 sheet: -0.45 (0.33), residues: 223 loop : 0.06 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.022 0.001 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8260) covalent geometry : angle 0.52001 (11204) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.34314 ( 6) hydrogen bonds : bond 0.04052 ( 454) hydrogen bonds : angle 4.40084 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.33 seconds wall clock time: 36 minutes 8.14 seconds (2168.14 seconds total)