Starting phenix.real_space_refine on Sat Aug 23 05:56:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuv_29481/08_2025/8fuv_29481.cif" } resolution = 3.1 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= 0.001 sd= 0.006 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 36 5.16 5 C 6394 2.51 5 N 1755 2.21 5 O 1985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 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: 10170 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3780 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain: "T" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Time building chain proxies: 1.99, per 1000 atoms: 0.20 Number of scatterers: 10170 At special positions: 0 Unit cell: (162.4, 129.92, 82.88, 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 36 16.00 O 1985 8.00 N 1755 7.00 C 6394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 413.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 21.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'F' and resid 46 through 55 removed outlier: 3.554A pdb=" N VAL F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.511A pdb=" N GLN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 150 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.304A pdb=" N GLN F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 removed outlier: 3.613A pdb=" N ALA F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.542A pdb=" N ALA F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 254 Processing helix chain 'F' and resid 265 through 276 removed outlier: 4.244A pdb=" N GLY F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 275 " --> pdb=" O THR F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.594A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.753A pdb=" N SER F 342 " --> pdb=" O THR F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 398 Processing helix chain 'F' and resid 405 through 427 Proline residue: F 418 - end of helix Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 451 through 459 removed outlier: 3.785A pdb=" N GLN F 455 " --> pdb=" O ARG F 451 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 45 No H-bonds generated for 'chain 'T' and resid 43 through 45' Processing helix chain 'T' and resid 66 through 80 removed outlier: 3.707A pdb=" N ASN T 79 " --> pdb=" O LEU T 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 66 through 80 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 66 through 80 Processing sheet with id=AA1, first strand: chain 'F' and resid 42 through 44 removed outlier: 6.408A pdb=" N ARG F 28 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.591A pdb=" N THR F 171 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 172 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'F' and resid 260 through 264 removed outlier: 6.492A pdb=" N TYR F 260 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN F 285 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL F 262 " --> pdb=" O ASN F 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 Processing sheet with id=AA6, first strand: chain 'F' and resid 461 through 471 Processing sheet with id=AA7, first strand: chain 'T' and resid 17 through 19 removed outlier: 6.476A pdb=" N VAL T 92 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN T 108 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG T 134 " --> pdb=" O THR T 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU T 56 " --> pdb=" O PHE T 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 17 through 19 removed outlier: 6.476A pdb=" N VAL T 92 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN T 108 " --> pdb=" O VAL T 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'T' and resid 37 through 41 Processing sheet with id=AB2, first strand: chain 'T' and resid 113 through 114 Processing sheet with id=AB3, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.431A pdb=" N VAL A 92 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 108 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.431A pdb=" N VAL A 92 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 108 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AB6, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.461A pdb=" N VAL B 92 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN B 108 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 134 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.461A pdb=" N VAL B 92 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN B 108 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AC2, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.403A pdb=" N VAL C 92 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN C 108 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.403A pdb=" N VAL C 92 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN C 108 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AC7, first strand: chain 'D' and resid 17 through 19 removed outlier: 6.373A pdb=" N VAL D 92 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 108 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 134 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 17 through 19 removed outlier: 6.373A pdb=" N VAL D 92 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 108 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.382A pdb=" N VAL E 92 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN E 108 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 134 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.382A pdb=" N VAL E 92 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN E 108 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 37 through 41 454 hydrogen bonds defined for protein. 1236 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: 1.62 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3443 1.34 - 1.46: 2019 1.46 - 1.58: 4826 1.58 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 10347 Sorted by residual: bond pdb=" CA ASP D 84 " pdb=" CB ASP D 84 " ideal model delta sigma weight residual 1.524 1.576 -0.052 1.62e-02 3.81e+03 1.03e+01 bond pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CA GLN F 417 " pdb=" C GLN F 417 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 9.19e-01 bond pdb=" N PRO F 101 " pdb=" CA PRO F 101 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 8.84e-01 bond pdb=" CG1 ILE T 112 " pdb=" CD1 ILE T 112 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.42e-01 ... (remaining 10342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13653 1.43 - 2.87: 354 2.87 - 4.30: 75 4.30 - 5.74: 10 5.74 - 7.17: 5 Bond angle restraints: 14097 Sorted by residual: angle pdb=" C ASN F 293 " pdb=" N ASP F 294 " pdb=" CA ASP F 294 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 angle pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " pdb=" CD LYS B 83 " ideal model delta sigma weight residual 111.30 118.26 -6.96 2.30e+00 1.89e-01 9.16e+00 angle pdb=" CA LYS B 83 " pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 angle pdb=" C GLY F 13 " pdb=" N VAL F 14 " pdb=" CA VAL F 14 " ideal model delta sigma weight residual 122.97 120.41 2.56 9.80e-01 1.04e+00 6.84e+00 angle pdb=" CG1 ILE T 29 " pdb=" CB ILE T 29 " pdb=" CG2 ILE T 29 " ideal model delta sigma weight residual 110.70 103.53 7.17 3.00e+00 1.11e-01 5.71e+00 ... (remaining 14092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 5532 15.22 - 30.43: 481 30.43 - 45.65: 121 45.65 - 60.86: 20 60.86 - 76.08: 11 Dihedral angle restraints: 6165 sinusoidal: 2282 harmonic: 3883 Sorted by residual: dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N ALA B 24 " pdb=" CA ALA B 24 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE E 23 " pdb=" C PHE E 23 " pdb=" N ALA E 24 " pdb=" CA ALA E 24 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE T 23 " pdb=" C PHE T 23 " pdb=" N ALA T 24 " pdb=" CA ALA T 24 " ideal model delta harmonic sigma weight residual -180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 6162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1197 0.042 - 0.083: 312 0.083 - 0.125: 136 0.125 - 0.166: 16 0.166 - 0.208: 3 Chirality restraints: 1664 Sorted by residual: chirality pdb=" CB ILE T 29 " pdb=" CA ILE T 29 " pdb=" CG1 ILE T 29 " pdb=" CG2 ILE T 29 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 29 " pdb=" CA ILE A 29 " pdb=" CG1 ILE A 29 " pdb=" CG2 ILE A 29 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 1661 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 63 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 64 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 63 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO D 64 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 63 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 64 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.024 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 379 2.72 - 3.26: 9612 3.26 - 3.81: 15117 3.81 - 4.35: 18531 4.35 - 4.90: 32730 Nonbonded interactions: 76369 Sorted by model distance: nonbonded pdb=" OD2 ASP F 192 " pdb=" OG SER F 194 " model vdw 2.169 3.040 nonbonded pdb=" OG SER F 72 " pdb=" O SER F 74 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR F 162 " pdb=" OG1 THR F 171 " model vdw 2.296 3.040 nonbonded pdb=" O ASN F 255 " pdb=" NZ LYS F 385 " model vdw 2.306 3.120 nonbonded pdb=" OD1 ASN F 285 " pdb=" OH TYR F 360 " model vdw 2.358 3.040 ... (remaining 76364 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.230 Find NCS groups from input model: 0.120 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.003 0.052 10347 Z= 0.150 Angle : 0.590 7.171 14097 Z= 0.337 Chirality : 0.045 0.208 1664 Planarity : 0.004 0.044 1857 Dihedral : 12.825 76.078 3667 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.17 (0.22), residues: 1354 helix: 3.23 (0.34), residues: 236 sheet: 0.46 (0.26), residues: 403 loop : -1.72 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 134 TYR 0.010 0.001 TYR F 67 PHE 0.012 0.001 PHE E 34 TRP 0.007 0.001 TRP F 462 Details of bonding type rmsd covalent geometry : bond 0.00309 (10347) covalent geometry : angle 0.58985 (14097) hydrogen bonds : bond 0.20700 ( 370) hydrogen bonds : angle 6.32283 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.427 Fit side-chains REVERT: F 137 MET cc_start: 0.7539 (pmm) cc_final: 0.7195 (pmm) REVERT: F 490 LYS cc_start: 0.5579 (mptt) cc_final: 0.5189 (mmtt) REVERT: E 23 PHE cc_start: 0.5933 (t80) cc_final: 0.5695 (t80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1266 time to fit residues: 26.5268 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075039 restraints weight = 23614.922| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.64 r_work: 0.2968 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10347 Z= 0.134 Angle : 0.541 6.199 14097 Z= 0.301 Chirality : 0.045 0.142 1664 Planarity : 0.004 0.044 1857 Dihedral : 4.479 20.297 1447 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.74 % Allowed : 6.46 % Favored : 92.80 % 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: -0.31 (0.22), residues: 1354 helix: 2.62 (0.33), residues: 252 sheet: 0.27 (0.25), residues: 465 loop : -1.83 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 134 TYR 0.011 0.001 TYR F 67 PHE 0.012 0.002 PHE E 34 TRP 0.011 0.001 TRP F 250 Details of bonding type rmsd covalent geometry : bond 0.00300 (10347) covalent geometry : angle 0.54110 (14097) hydrogen bonds : bond 0.05059 ( 370) hydrogen bonds : angle 4.71416 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.316 Fit side-chains REVERT: F 490 LYS cc_start: 0.6060 (mptt) cc_final: 0.5374 (mmtt) REVERT: E 23 PHE cc_start: 0.6852 (t80) cc_final: 0.6470 (t80) outliers start: 8 outliers final: 5 residues processed: 151 average time/residue: 0.1281 time to fit residues: 25.4285 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN C 79 ASN D 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071998 restraints weight = 23383.450| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.56 r_work: 0.2907 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10347 Z= 0.199 Angle : 0.583 5.566 14097 Z= 0.328 Chirality : 0.047 0.173 1664 Planarity : 0.005 0.052 1857 Dihedral : 4.974 27.253 1447 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.29 % Allowed : 9.87 % Favored : 88.84 % 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: -0.47 (0.22), residues: 1354 helix: 2.47 (0.34), residues: 253 sheet: 0.01 (0.24), residues: 475 loop : -1.81 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 134 TYR 0.013 0.002 TYR F 67 PHE 0.016 0.002 PHE E 34 TRP 0.008 0.001 TRP F 250 Details of bonding type rmsd covalent geometry : bond 0.00479 (10347) covalent geometry : angle 0.58342 (14097) hydrogen bonds : bond 0.05648 ( 370) hydrogen bonds : angle 4.48397 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.411 Fit side-chains REVERT: F 137 MET cc_start: 0.7628 (pmm) cc_final: 0.7240 (pmm) REVERT: F 490 LYS cc_start: 0.6134 (mptt) cc_final: 0.5570 (mptt) REVERT: T 69 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 25 ASP cc_start: 0.8352 (p0) cc_final: 0.8146 (p0) REVERT: E 23 PHE cc_start: 0.6804 (t80) cc_final: 0.6445 (t80) outliers start: 14 outliers final: 4 residues processed: 160 average time/residue: 0.1256 time to fit residues: 26.8090 Evaluate side-chains 147 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073077 restraints weight = 23633.617| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.62 r_work: 0.2925 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10347 Z= 0.149 Angle : 0.531 5.923 14097 Z= 0.296 Chirality : 0.046 0.153 1664 Planarity : 0.005 0.050 1857 Dihedral : 4.720 22.281 1447 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.57 % Allowed : 11.72 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.22), residues: 1354 helix: 2.46 (0.33), residues: 253 sheet: -0.11 (0.24), residues: 475 loop : -1.79 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.011 0.001 TYR F 67 PHE 0.013 0.002 PHE E 34 TRP 0.008 0.001 TRP F 250 Details of bonding type rmsd covalent geometry : bond 0.00349 (10347) covalent geometry : angle 0.53103 (14097) hydrogen bonds : bond 0.04691 ( 370) hydrogen bonds : angle 4.16576 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.298 Fit side-chains REVERT: F 137 MET cc_start: 0.7669 (pmm) cc_final: 0.7296 (pmm) REVERT: F 490 LYS cc_start: 0.6074 (mptt) cc_final: 0.5554 (mptt) REVERT: T 23 PHE cc_start: 0.7005 (t80) cc_final: 0.6730 (t80) REVERT: B 23 PHE cc_start: 0.6943 (t80) cc_final: 0.6692 (t80) REVERT: C 23 PHE cc_start: 0.6738 (t80) cc_final: 0.6464 (t80) REVERT: C 30 ASP cc_start: 0.8693 (t0) cc_final: 0.8484 (t0) REVERT: D 23 PHE cc_start: 0.7178 (t80) cc_final: 0.6871 (t80) REVERT: E 23 PHE cc_start: 0.6834 (t80) cc_final: 0.6483 (t80) outliers start: 17 outliers final: 6 residues processed: 150 average time/residue: 0.1271 time to fit residues: 25.5006 Evaluate side-chains 142 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070654 restraints weight = 23562.600| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.60 r_work: 0.2893 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10347 Z= 0.196 Angle : 0.579 6.166 14097 Z= 0.325 Chirality : 0.047 0.179 1664 Planarity : 0.005 0.053 1857 Dihedral : 5.016 24.357 1447 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 1.48 % Allowed : 12.55 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.22), residues: 1354 helix: 2.43 (0.34), residues: 253 sheet: -0.16 (0.24), residues: 481 loop : -1.81 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 134 TYR 0.013 0.002 TYR F 67 PHE 0.016 0.002 PHE E 34 TRP 0.007 0.001 TRP F 250 Details of bonding type rmsd covalent geometry : bond 0.00472 (10347) covalent geometry : angle 0.57851 (14097) hydrogen bonds : bond 0.05381 ( 370) hydrogen bonds : angle 4.15552 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.325 Fit side-chains REVERT: F 137 MET cc_start: 0.7478 (pmm) cc_final: 0.7233 (pmm) REVERT: F 490 LYS cc_start: 0.6574 (mptt) cc_final: 0.6059 (mptt) REVERT: T 69 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 23 PHE cc_start: 0.6845 (t80) cc_final: 0.6555 (t80) REVERT: C 30 ASP cc_start: 0.8702 (t0) cc_final: 0.8480 (t0) REVERT: D 23 PHE cc_start: 0.7190 (t80) cc_final: 0.6943 (t80) REVERT: E 23 PHE cc_start: 0.6868 (t80) cc_final: 0.6523 (t80) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.1198 time to fit residues: 24.5747 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 0.0070 chunk 106 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072929 restraints weight = 23602.530| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.63 r_work: 0.2936 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10347 Z= 0.122 Angle : 0.510 6.434 14097 Z= 0.282 Chirality : 0.045 0.141 1664 Planarity : 0.005 0.049 1857 Dihedral : 4.587 20.605 1447 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 1.75 % Allowed : 12.36 % Favored : 85.89 % 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: -0.56 (0.22), residues: 1354 helix: 2.50 (0.33), residues: 253 sheet: -0.17 (0.24), residues: 475 loop : -1.80 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.011 0.001 TYR F 67 PHE 0.010 0.001 PHE E 34 TRP 0.009 0.001 TRP F 199 Details of bonding type rmsd covalent geometry : bond 0.00269 (10347) covalent geometry : angle 0.50971 (14097) hydrogen bonds : bond 0.04219 ( 370) hydrogen bonds : angle 3.96091 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.422 Fit side-chains REVERT: F 137 MET cc_start: 0.7670 (pmm) cc_final: 0.7342 (pmm) REVERT: F 490 LYS cc_start: 0.6531 (mptt) cc_final: 0.5976 (mptt) REVERT: A 23 PHE cc_start: 0.6793 (t80) cc_final: 0.6523 (t80) REVERT: C 23 PHE cc_start: 0.6829 (t80) cc_final: 0.6541 (t80) REVERT: C 30 ASP cc_start: 0.8657 (t0) cc_final: 0.8437 (t0) REVERT: D 23 PHE cc_start: 0.7101 (t80) cc_final: 0.6867 (t80) REVERT: E 23 PHE cc_start: 0.6884 (t80) cc_final: 0.6483 (t80) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.1199 time to fit residues: 24.4808 Evaluate side-chains 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070494 restraints weight = 23432.926| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.60 r_work: 0.2884 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10347 Z= 0.200 Angle : 0.574 6.907 14097 Z= 0.322 Chirality : 0.047 0.172 1664 Planarity : 0.005 0.054 1857 Dihedral : 4.934 22.830 1447 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Rotamer: Outliers : 2.58 % Allowed : 11.99 % Favored : 85.42 % 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: -0.60 (0.22), residues: 1354 helix: 2.40 (0.34), residues: 253 sheet: -0.18 (0.24), residues: 481 loop : -1.82 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.013 0.002 TYR F 67 PHE 0.015 0.002 PHE E 34 TRP 0.007 0.001 TRP F 250 Details of bonding type rmsd covalent geometry : bond 0.00484 (10347) covalent geometry : angle 0.57442 (14097) hydrogen bonds : bond 0.05237 ( 370) hydrogen bonds : angle 4.08934 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.468 Fit side-chains REVERT: F 179 THR cc_start: 0.8216 (m) cc_final: 0.7913 (t) REVERT: F 490 LYS cc_start: 0.6429 (mptt) cc_final: 0.6029 (mptt) REVERT: T 8 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9102 (p) REVERT: T 69 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 23 PHE cc_start: 0.6908 (t80) cc_final: 0.6651 (t80) REVERT: C 23 PHE cc_start: 0.6933 (t80) cc_final: 0.6629 (t80) REVERT: C 30 ASP cc_start: 0.8679 (t0) cc_final: 0.8463 (t0) REVERT: D 23 PHE cc_start: 0.7145 (t80) cc_final: 0.6928 (t80) REVERT: E 23 PHE cc_start: 0.6905 (t80) cc_final: 0.6529 (t80) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.1135 time to fit residues: 25.4420 Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 70 optimal weight: 40.0000 chunk 122 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.069943 restraints weight = 23587.601| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.61 r_work: 0.2872 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10347 Z= 0.211 Angle : 0.594 7.275 14097 Z= 0.333 Chirality : 0.048 0.184 1664 Planarity : 0.005 0.054 1857 Dihedral : 5.053 22.240 1447 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 2.58 % Allowed : 12.82 % Favored : 84.59 % 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: -0.68 (0.22), residues: 1354 helix: 2.25 (0.34), residues: 253 sheet: -0.23 (0.24), residues: 481 loop : -1.83 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 149 TYR 0.013 0.002 TYR F 67 PHE 0.016 0.002 PHE E 34 TRP 0.008 0.001 TRP F 199 Details of bonding type rmsd covalent geometry : bond 0.00510 (10347) covalent geometry : angle 0.59398 (14097) hydrogen bonds : bond 0.05388 ( 370) hydrogen bonds : angle 4.10785 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.417 Fit side-chains REVERT: F 319 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.7662 (tmm) REVERT: F 490 LYS cc_start: 0.6433 (mptt) cc_final: 0.6021 (mptt) REVERT: T 8 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9090 (p) REVERT: T 69 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 23 PHE cc_start: 0.6776 (t80) cc_final: 0.6544 (t80) REVERT: B 25 ASP cc_start: 0.8204 (p0) cc_final: 0.8003 (p0) REVERT: C 23 PHE cc_start: 0.6954 (t80) cc_final: 0.6634 (t80) REVERT: C 30 ASP cc_start: 0.8696 (t0) cc_final: 0.8483 (t0) REVERT: E 23 PHE cc_start: 0.6948 (t80) cc_final: 0.6591 (t80) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.1094 time to fit residues: 24.4006 Evaluate side-chains 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 0.0050 chunk 130 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074747 restraints weight = 23259.997| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.63 r_work: 0.2974 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10347 Z= 0.100 Angle : 0.502 7.283 14097 Z= 0.275 Chirality : 0.045 0.246 1664 Planarity : 0.004 0.048 1857 Dihedral : 4.343 28.246 1447 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.24 % Favored : 94.31 % Rotamer: Outliers : 1.20 % Allowed : 14.58 % Favored : 84.23 % 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: -0.63 (0.22), residues: 1354 helix: 2.48 (0.33), residues: 252 sheet: -0.26 (0.24), residues: 475 loop : -1.81 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 149 TYR 0.012 0.001 TYR F 360 PHE 0.022 0.001 PHE D 23 TRP 0.009 0.001 TRP F 462 Details of bonding type rmsd covalent geometry : bond 0.00202 (10347) covalent geometry : angle 0.50207 (14097) hydrogen bonds : bond 0.03464 ( 370) hydrogen bonds : angle 3.80054 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.405 Fit side-chains REVERT: F 75 VAL cc_start: 0.8324 (t) cc_final: 0.8049 (m) REVERT: F 179 THR cc_start: 0.8231 (m) cc_final: 0.7929 (t) REVERT: F 319 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8300 (tmm) REVERT: T 8 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (p) REVERT: A 23 PHE cc_start: 0.6715 (t80) cc_final: 0.6453 (t80) REVERT: C 23 PHE cc_start: 0.6817 (t80) cc_final: 0.6492 (t80) REVERT: E 23 PHE cc_start: 0.6869 (t80) cc_final: 0.6495 (t80) outliers start: 13 outliers final: 9 residues processed: 150 average time/residue: 0.1101 time to fit residues: 22.1895 Evaluate side-chains 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 119 optimal weight: 7.9990 chunk 68 optimal weight: 0.0970 chunk 124 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 61 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 125 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 = 0.3362 r_free = 0.3362 target = 0.091381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073497 restraints weight = 23057.402| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.61 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10347 Z= 0.116 Angle : 0.509 7.590 14097 Z= 0.281 Chirality : 0.044 0.215 1664 Planarity : 0.005 0.049 1857 Dihedral : 4.330 25.104 1447 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.32 % Favored : 94.24 % Rotamer: Outliers : 1.29 % Allowed : 15.04 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.23), residues: 1354 helix: 2.63 (0.34), residues: 252 sheet: -0.17 (0.25), residues: 475 loop : -1.78 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 149 TYR 0.011 0.001 TYR F 67 PHE 0.009 0.001 PHE T 133 TRP 0.007 0.001 TRP F 462 Details of bonding type rmsd covalent geometry : bond 0.00257 (10347) covalent geometry : angle 0.50855 (14097) hydrogen bonds : bond 0.03892 ( 370) hydrogen bonds : angle 3.76614 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.405 Fit side-chains REVERT: F 179 THR cc_start: 0.8351 (m) cc_final: 0.8049 (t) REVERT: F 319 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8287 (tmm) REVERT: T 8 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 23 PHE cc_start: 0.6769 (t80) cc_final: 0.6503 (t80) REVERT: C 23 PHE cc_start: 0.6864 (t80) cc_final: 0.6540 (t80) REVERT: E 23 PHE cc_start: 0.6860 (t80) cc_final: 0.6499 (t80) outliers start: 14 outliers final: 11 residues processed: 146 average time/residue: 0.1218 time to fit residues: 23.8506 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 100 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 125 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 = 0.3343 r_free = 0.3343 target = 0.090305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072323 restraints weight = 23364.910| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.63 r_work: 0.2926 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10347 Z= 0.141 Angle : 0.537 7.614 14097 Z= 0.299 Chirality : 0.045 0.219 1664 Planarity : 0.005 0.050 1857 Dihedral : 4.523 26.834 1447 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Rotamer: Outliers : 1.66 % Allowed : 14.85 % Favored : 83.49 % 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: -0.52 (0.23), residues: 1354 helix: 2.58 (0.34), residues: 253 sheet: -0.16 (0.25), residues: 475 loop : -1.79 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 134 TYR 0.012 0.001 TYR F 67 PHE 0.023 0.002 PHE B 23 TRP 0.007 0.001 TRP F 462 Details of bonding type rmsd covalent geometry : bond 0.00327 (10347) covalent geometry : angle 0.53693 (14097) hydrogen bonds : bond 0.04287 ( 370) hydrogen bonds : angle 3.81495 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.54 seconds wall clock time: 46 minutes 5.15 seconds (2765.15 seconds total)