Starting phenix.real_space_refine on Fri Jun 6 18:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flt_29286/06_2025/8flt_29286_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flt_29286/06_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_29286/06_2025/8flt_29286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flt_29286/06_2025/8flt_29286.map" model { file = "/net/cci-nas-00/data/ceres_data/8flt_29286/06_2025/8flt_29286_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flt_29286/06_2025/8flt_29286_neut.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLU:plan': 2, 'ARG: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: {'HRG:plan-2': 1, 'AIB:plan-1': 2} 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: 5.24, per 1000 atoms: 0.65 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.43 Time building geometry restraints manager: 2.33 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (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 TRP 0.018 0.002 TRP R 298 HIS 0.008 0.002 HIS A 357 PHE 0.026 0.002 PHE R 335 TYR 0.012 0.002 TYR B 59 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.14119 ( 454) hydrogen bonds : angle 6.35044 ( 1293) SS BOND : bond 0.00206 ( 3) SS BOND : angle 1.67729 ( 6) covalent geometry : bond 0.00441 ( 8260) covalent geometry : angle 0.66582 (11204) *********************** 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 : 0.819 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2292 time to fit residues: 38.9647 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 : 0.819 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** R 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.135661 restraints weight = 8887.389| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.33 r_work: 0.3324 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8263 Z= 0.131 Angle : 0.515 5.528 11210 Z= 0.288 Chirality : 0.042 0.178 1257 Planarity : 0.004 0.039 1422 Dihedral : 5.218 58.096 1128 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.71 % Allowed : 5.31 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1005 helix: 2.45 (0.26), residues: 397 sheet: -0.58 (0.33), residues: 219 loop : -0.21 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.030 0.002 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 454) hydrogen bonds : angle 4.74011 ( 1293) SS BOND : bond 0.00526 ( 3) SS BOND : angle 1.73004 ( 6) covalent geometry : bond 0.00283 ( 8260) covalent geometry : angle 0.51374 (11204) *********************** 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 : 0.886 Fit side-chains REVERT: B 138 GLU cc_start: 0.7290 (tt0) cc_final: 0.6981 (pm20) REVERT: N 95 TYR cc_start: 0.7809 (m-80) cc_final: 0.7596 (m-80) outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.2411 time to fit residues: 39.4789 Evaluate side-chains 118 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.138443 restraints weight = 8988.346| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.41 r_work: 0.3336 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8263 Z= 0.108 Angle : 0.474 5.367 11210 Z= 0.266 Chirality : 0.040 0.171 1257 Planarity : 0.003 0.040 1422 Dihedral : 4.954 58.206 1128 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.94 % Allowed : 7.32 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 1005 helix: 2.75 (0.26), residues: 389 sheet: -0.46 (0.34), residues: 206 loop : -0.05 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 454) hydrogen bonds : angle 4.48065 ( 1293) SS BOND : bond 0.00469 ( 3) SS BOND : angle 1.74977 ( 6) covalent geometry : bond 0.00225 ( 8260) covalent geometry : angle 0.47282 (11204) *********************** 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 130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.887 Fit side-chains REVERT: B 135 VAL cc_start: 0.7422 (t) cc_final: 0.7153 (p) REVERT: B 138 GLU cc_start: 0.7327 (tt0) cc_final: 0.6855 (pm20) REVERT: G 17 GLU cc_start: 0.7801 (mp0) cc_final: 0.7583 (mp0) REVERT: N 59 SER cc_start: 0.7815 (t) cc_final: 0.7200 (p) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.2658 time to fit residues: 44.2191 Evaluate side-chains 119 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 274 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 377 ASN ** 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 = 0.3687 r_free = 0.3687 target = 0.159080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.134211 restraints weight = 8995.665| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.43 r_work: 0.3287 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1348 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= 0.139 Angle : 0.501 5.471 11210 Z= 0.278 Chirality : 0.042 0.177 1257 Planarity : 0.004 0.043 1422 Dihedral : 5.007 58.078 1128 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.94 % Allowed : 7.67 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 1005 helix: 2.63 (0.26), residues: 395 sheet: -0.49 (0.33), residues: 219 loop : -0.12 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.029 0.002 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 454) hydrogen bonds : angle 4.48034 ( 1293) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.93280 ( 6) covalent geometry : bond 0.00315 ( 8260) covalent geometry : angle 0.49942 (11204) *********************** 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 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.900 Fit side-chains REVERT: A 374 ARG cc_start: 0.6628 (ttm170) cc_final: 0.5713 (ttm110) REVERT: A 378 ASP cc_start: 0.7022 (m-30) cc_final: 0.6763 (m-30) REVERT: B 135 VAL cc_start: 0.7607 (t) cc_final: 0.7338 (p) REVERT: B 138 GLU cc_start: 0.7431 (tt0) cc_final: 0.7003 (pm20) REVERT: N 19 ARG cc_start: 0.7416 (ttt90) cc_final: 0.7181 (ttm170) REVERT: N 95 TYR cc_start: 0.7843 (m-80) cc_final: 0.7565 (m-80) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.2491 time to fit residues: 40.6246 Evaluate side-chains 119 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 0.0040 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.160999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.136380 restraints weight = 8960.557| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.43 r_work: 0.3320 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8263 Z= 0.110 Angle : 0.478 6.419 11210 Z= 0.267 Chirality : 0.041 0.172 1257 Planarity : 0.003 0.042 1422 Dihedral : 4.856 59.142 1128 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.30 % Allowed : 8.26 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1005 helix: 2.99 (0.26), residues: 383 sheet: -0.40 (0.33), residues: 219 loop : 0.07 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 454) hydrogen bonds : angle 4.37032 ( 1293) SS BOND : bond 0.00314 ( 3) SS BOND : angle 2.35715 ( 6) covalent geometry : bond 0.00233 ( 8260) covalent geometry : angle 0.47473 (11204) *********************** 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 132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.848 Fit side-chains REVERT: A 374 ARG cc_start: 0.6582 (ttm170) cc_final: 0.6186 (ttm-80) REVERT: A 378 ASP cc_start: 0.7015 (m-30) cc_final: 0.6769 (m-30) REVERT: B 135 VAL cc_start: 0.7644 (t) cc_final: 0.7393 (p) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.2414 time to fit residues: 39.6876 Evaluate side-chains 119 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128513 restraints weight = 8978.437| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.45 r_work: 0.3234 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8263 Z= 0.197 Angle : 0.565 5.926 11210 Z= 0.310 Chirality : 0.044 0.185 1257 Planarity : 0.004 0.046 1422 Dihedral : 5.193 57.315 1128 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1005 helix: 2.43 (0.26), residues: 395 sheet: -0.54 (0.33), residues: 222 loop : -0.18 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.008 0.001 HIS A 357 PHE 0.030 0.002 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 454) hydrogen bonds : angle 4.63868 ( 1293) SS BOND : bond 0.00431 ( 3) SS BOND : angle 2.31462 ( 6) covalent geometry : bond 0.00463 ( 8260) covalent geometry : angle 0.56276 (11204) *********************** 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 130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.920 Fit side-chains REVERT: A 347 ARG cc_start: 0.6127 (tpp80) cc_final: 0.5377 (tmm160) REVERT: A 374 ARG cc_start: 0.6847 (ttm170) cc_final: 0.6433 (ttm110) REVERT: A 378 ASP cc_start: 0.7254 (m-30) cc_final: 0.6970 (m-30) REVERT: B 135 VAL cc_start: 0.7836 (t) cc_final: 0.7587 (p) REVERT: N 95 TYR cc_start: 0.7953 (m-80) cc_final: 0.7707 (m-80) REVERT: R 321 LEU cc_start: 0.7799 (tp) cc_final: 0.7593 (tp) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.2370 time to fit residues: 38.4916 Evaluate side-chains 124 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.159116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134332 restraints weight = 9011.243| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.38 r_work: 0.3278 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1601 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 : 0.488 5.502 11210 Z= 0.271 Chirality : 0.041 0.174 1257 Planarity : 0.003 0.043 1422 Dihedral : 4.954 58.001 1128 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.18 % Allowed : 10.15 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1005 helix: 2.63 (0.26), residues: 395 sheet: -0.57 (0.33), residues: 223 loop : -0.08 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.029 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 454) hydrogen bonds : angle 4.48012 ( 1293) SS BOND : bond 0.00329 ( 3) SS BOND : angle 1.71153 ( 6) covalent geometry : bond 0.00264 ( 8260) covalent geometry : angle 0.48602 (11204) *********************** 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 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7071 (m-30) cc_final: 0.6812 (m-30) REVERT: B 135 VAL cc_start: 0.7742 (t) cc_final: 0.7542 (p) REVERT: N 20 LEU cc_start: 0.7715 (mt) cc_final: 0.7395 (mt) REVERT: R 321 LEU cc_start: 0.7791 (tp) cc_final: 0.7563 (tp) outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 0.2563 time to fit residues: 43.1215 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 : 1.156 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.159970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135143 restraints weight = 9010.942| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.42 r_work: 0.3298 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8263 Z= 0.116 Angle : 0.486 6.086 11210 Z= 0.272 Chirality : 0.041 0.172 1257 Planarity : 0.003 0.043 1422 Dihedral : 4.851 57.831 1128 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.42 % Allowed : 9.92 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1005 helix: 2.95 (0.26), residues: 383 sheet: -0.56 (0.33), residues: 223 loop : 0.05 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.029 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.006 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 454) hydrogen bonds : angle 4.42301 ( 1293) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.61256 ( 6) covalent geometry : bond 0.00252 ( 8260) covalent geometry : angle 0.48493 (11204) *********************** 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 131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6504 (mt-10) REVERT: B 44 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8210 (mm-40) REVERT: N 20 LEU cc_start: 0.7682 (mt) cc_final: 0.7371 (mt) REVERT: R 321 LEU cc_start: 0.7738 (tp) cc_final: 0.7515 (tp) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.2534 time to fit residues: 40.9646 Evaluate side-chains 130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.158416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130903 restraints weight = 9126.332| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.47 r_work: 0.3296 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1708 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= 0.144 Angle : 0.515 6.334 11210 Z= 0.285 Chirality : 0.042 0.177 1257 Planarity : 0.003 0.042 1422 Dihedral : 4.953 57.698 1128 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.42 % Allowed : 10.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1005 helix: 2.75 (0.26), residues: 389 sheet: -0.58 (0.33), residues: 223 loop : -0.02 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS A 362 PHE 0.029 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 454) hydrogen bonds : angle 4.48508 ( 1293) SS BOND : bond 0.00265 ( 3) SS BOND : angle 1.65210 ( 6) covalent geometry : bond 0.00327 ( 8260) covalent geometry : angle 0.51329 (11204) *********************** 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: 12 poor density : 124 time to evaluate : 0.837 Fit side-chains REVERT: A 378 ASP cc_start: 0.7073 (m-30) cc_final: 0.6824 (m-30) REVERT: A 392 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6546 (mt-10) REVERT: B 44 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8211 (mm-40) REVERT: N 19 ARG cc_start: 0.7572 (tpt-90) cc_final: 0.7267 (ttt90) REVERT: N 95 TYR cc_start: 0.7834 (m-80) cc_final: 0.7479 (m-80) REVERT: R 321 LEU cc_start: 0.7823 (tp) cc_final: 0.7607 (tp) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.2486 time to fit residues: 41.9398 Evaluate side-chains 131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.161577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.137818 restraints weight = 8941.517| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.34 r_work: 0.3347 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8263 Z= 0.109 Angle : 0.484 7.395 11210 Z= 0.270 Chirality : 0.041 0.169 1257 Planarity : 0.003 0.042 1422 Dihedral : 4.783 57.982 1128 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.42 % Allowed : 10.86 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1005 helix: 3.04 (0.26), residues: 383 sheet: -0.43 (0.34), residues: 210 loop : 0.06 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 362 PHE 0.028 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.005 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 454) hydrogen bonds : angle 4.35856 ( 1293) SS BOND : bond 0.00240 ( 3) SS BOND : angle 1.35712 ( 6) covalent geometry : bond 0.00230 ( 8260) covalent geometry : angle 0.48323 (11204) ********************** 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 132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.840 Fit side-chains REVERT: A 392 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6508 (mt-10) REVERT: B 44 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8206 (mm-40) REVERT: N 20 LEU cc_start: 0.7617 (mt) cc_final: 0.7332 (mt) REVERT: R 321 LEU cc_start: 0.7816 (tp) cc_final: 0.7575 (tp) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.2522 time to fit residues: 40.7565 Evaluate side-chains 130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.0020 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.163306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.140277 restraints weight = 8966.325| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.28 r_work: 0.3327 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1856 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= 0.117 Angle : 0.499 12.244 11210 Z= 0.275 Chirality : 0.041 0.172 1257 Planarity : 0.003 0.043 1422 Dihedral : 4.782 57.463 1128 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.42 % Allowed : 11.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1005 helix: 3.00 (0.25), residues: 383 sheet: -0.51 (0.33), residues: 223 loop : 0.09 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 362 PHE 0.029 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 454) hydrogen bonds : angle 4.36345 ( 1293) SS BOND : bond 0.00209 ( 3) SS BOND : angle 1.35566 ( 6) covalent geometry : bond 0.00254 ( 8260) covalent geometry : angle 0.49769 (11204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.60 seconds wall clock time: 83 minutes 34.94 seconds (5014.94 seconds total)