Starting phenix.real_space_refine on Mon Jun 9 01:06:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuv_29481/06_2025/8fuv_29481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuv_29481/06_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_29481/06_2025/8fuv_29481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuv_29481/06_2025/8fuv_29481.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuv_29481/06_2025/8fuv_29481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuv_29481/06_2025/8fuv_29481.cif" } resolution = 3.1 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.41, per 1000 atoms: 0.63 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.59 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: 3.42 Time building geometry restraints manager: 3.02 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: 1.690 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- 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 (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: -0.17 (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 TRP 0.007 0.001 TRP F 462 PHE 0.012 0.001 PHE E 34 TYR 0.010 0.001 TYR F 67 ARG 0.003 0.000 ARG T 134 Details of bonding type rmsd hydrogen bonds : bond 0.20700 ( 370) hydrogen bonds : angle 6.32283 ( 1236) covalent geometry : bond 0.00309 (10347) covalent geometry : angle 0.58985 (14097) *********************** 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 : 1.059 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: 0.2932 time to fit residues: 61.5328 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 : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074001 restraints weight = 23250.998| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.60 r_work: 0.2957 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10347 Z= 0.151 Angle : 0.557 6.225 14097 Z= 0.311 Chirality : 0.046 0.149 1664 Planarity : 0.005 0.046 1857 Dihedral : 4.581 21.087 1447 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.74 % Allowed : 6.27 % Favored : 92.99 % 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: -0.33 (0.22), residues: 1354 helix: 2.57 (0.33), residues: 253 sheet: 0.26 (0.25), residues: 465 loop : -1.85 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 250 PHE 0.013 0.002 PHE E 34 TYR 0.012 0.001 TYR F 67 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 370) hydrogen bonds : angle 4.71557 ( 1236) covalent geometry : bond 0.00347 (10347) covalent geometry : angle 0.55663 (14097) *********************** 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 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.218 Fit side-chains REVERT: F 490 LYS cc_start: 0.6100 (mptt) cc_final: 0.5844 (mptt) REVERT: E 23 PHE cc_start: 0.6808 (t80) cc_final: 0.6448 (t80) outliers start: 8 outliers final: 6 residues processed: 152 average time/residue: 0.2901 time to fit residues: 58.4125 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 VAL 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 78 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072494 restraints weight = 23750.310| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.63 r_work: 0.2914 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10347 Z= 0.180 Angle : 0.567 5.651 14097 Z= 0.319 Chirality : 0.046 0.163 1664 Planarity : 0.005 0.052 1857 Dihedral : 4.874 26.262 1447 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.57 % Allowed : 9.87 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1354 helix: 2.50 (0.34), residues: 253 sheet: 0.02 (0.24), residues: 475 loop : -1.82 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 250 PHE 0.019 0.002 PHE B 23 TYR 0.012 0.001 TYR F 67 ARG 0.004 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 370) hydrogen bonds : angle 4.44516 ( 1236) covalent geometry : bond 0.00431 (10347) covalent geometry : angle 0.56654 (14097) *********************** 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 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.103 Fit side-chains REVERT: F 137 MET cc_start: 0.7628 (pmm) cc_final: 0.7234 (pmm) REVERT: F 490 LYS cc_start: 0.6129 (mptt) cc_final: 0.5619 (mptt) REVERT: T 69 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 23 PHE cc_start: 0.6866 (t80) cc_final: 0.6581 (t80) REVERT: E 23 PHE cc_start: 0.6825 (t80) cc_final: 0.6457 (t80) outliers start: 17 outliers final: 5 residues processed: 161 average time/residue: 0.3157 time to fit residues: 68.7312 Evaluate side-chains 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 VAL 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 84 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.071780 restraints weight = 23225.998| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.60 r_work: 0.2916 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10347 Z= 0.174 Angle : 0.555 6.115 14097 Z= 0.311 Chirality : 0.046 0.168 1664 Planarity : 0.005 0.052 1857 Dihedral : 4.864 23.906 1447 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.66 % Allowed : 11.53 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1354 helix: 2.44 (0.33), residues: 253 sheet: -0.10 (0.24), residues: 475 loop : -1.80 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 250 PHE 0.014 0.002 PHE E 34 TYR 0.012 0.001 TYR F 67 ARG 0.004 0.000 ARG D 134 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 370) hydrogen bonds : angle 4.21822 ( 1236) covalent geometry : bond 0.00414 (10347) covalent geometry : angle 0.55536 (14097) *********************** 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 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.052 Fit side-chains REVERT: F 137 MET cc_start: 0.7620 (pmm) cc_final: 0.7244 (pmm) REVERT: F 490 LYS cc_start: 0.6084 (mptt) cc_final: 0.5492 (mptt) REVERT: T 69 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 23 PHE cc_start: 0.6918 (t80) cc_final: 0.6629 (t80) REVERT: B 23 PHE cc_start: 0.7034 (t80) cc_final: 0.6741 (t80) REVERT: C 30 ASP cc_start: 0.8741 (t0) cc_final: 0.8517 (t0) REVERT: D 23 PHE cc_start: 0.7195 (t80) cc_final: 0.6885 (t80) REVERT: E 23 PHE cc_start: 0.6829 (t80) cc_final: 0.6475 (t80) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 0.2778 time to fit residues: 56.0290 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 : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 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 A residue 19 VAL Chi-restraints excluded: chain B residue 10 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 40.0000 chunk 108 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.090977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073052 restraints weight = 23164.364| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.60 r_work: 0.2938 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10347 Z= 0.128 Angle : 0.510 5.900 14097 Z= 0.283 Chirality : 0.045 0.140 1664 Planarity : 0.004 0.049 1857 Dihedral : 4.556 20.623 1447 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.48 % Allowed : 12.45 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1354 helix: 2.53 (0.33), residues: 253 sheet: -0.13 (0.24), residues: 475 loop : -1.80 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 462 PHE 0.011 0.001 PHE E 34 TYR 0.011 0.001 TYR F 67 ARG 0.003 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 370) hydrogen bonds : angle 4.02376 ( 1236) covalent geometry : bond 0.00292 (10347) covalent geometry : angle 0.51036 (14097) *********************** 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 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.133 Fit side-chains REVERT: F 137 MET cc_start: 0.7695 (pmm) cc_final: 0.7354 (pmm) REVERT: F 490 LYS cc_start: 0.6560 (mptt) cc_final: 0.6023 (mptt) REVERT: A 23 PHE cc_start: 0.6887 (t80) cc_final: 0.6594 (t80) REVERT: C 23 PHE cc_start: 0.6837 (t80) cc_final: 0.6528 (t80) REVERT: C 30 ASP cc_start: 0.8663 (t0) cc_final: 0.8445 (t0) REVERT: D 23 PHE cc_start: 0.7162 (t80) cc_final: 0.6878 (t80) REVERT: E 23 PHE cc_start: 0.6879 (t80) cc_final: 0.6482 (t80) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.2948 time to fit residues: 59.0027 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 : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 19 VAL Chi-restraints excluded: chain A residue 138 VAL 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 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 109 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.070180 restraints weight = 23542.634| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.60 r_work: 0.2883 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10347 Z= 0.216 Angle : 0.591 6.574 14097 Z= 0.332 Chirality : 0.047 0.183 1664 Planarity : 0.005 0.054 1857 Dihedral : 5.031 22.583 1447 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.76 % Favored : 93.80 % Rotamer: Outliers : 2.31 % Allowed : 12.08 % Favored : 85.61 % 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: -0.61 (0.22), residues: 1354 helix: 2.41 (0.34), residues: 253 sheet: -0.20 (0.24), residues: 481 loop : -1.83 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 PHE 0.017 0.002 PHE E 34 TYR 0.013 0.002 TYR F 67 ARG 0.004 0.001 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 370) hydrogen bonds : angle 4.16128 ( 1236) covalent geometry : bond 0.00524 (10347) covalent geometry : angle 0.59129 (14097) *********************** 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 168 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.265 Fit side-chains REVERT: F 137 MET cc_start: 0.7437 (pmm) cc_final: 0.7204 (pmm) REVERT: F 179 THR cc_start: 0.8198 (m) cc_final: 0.7881 (t) REVERT: F 490 LYS cc_start: 0.6553 (mptt) cc_final: 0.6016 (mptt) REVERT: T 8 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (p) REVERT: T 69 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 23 PHE cc_start: 0.6990 (t80) cc_final: 0.6721 (t80) REVERT: C 23 PHE cc_start: 0.6935 (t80) cc_final: 0.6629 (t80) REVERT: C 30 ASP cc_start: 0.8709 (t0) cc_final: 0.8473 (t0) REVERT: D 23 PHE cc_start: 0.7190 (t80) cc_final: 0.6939 (t80) REVERT: E 23 PHE cc_start: 0.6931 (t80) cc_final: 0.6561 (t80) outliers start: 25 outliers final: 18 residues processed: 167 average time/residue: 0.2936 time to fit residues: 66.3048 Evaluate side-chains 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 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 C 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 18 THR 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 127 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 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 99 ASN F 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069905 restraints weight = 23761.673| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.62 r_work: 0.2868 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10347 Z= 0.210 Angle : 0.590 6.758 14097 Z= 0.332 Chirality : 0.047 0.190 1664 Planarity : 0.005 0.054 1857 Dihedral : 5.077 23.912 1447 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Rotamer: Outliers : 2.68 % Allowed : 12.27 % Favored : 85.06 % 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 (0.22), residues: 1354 helix: 2.28 (0.33), residues: 253 sheet: -0.22 (0.24), residues: 481 loop : -1.83 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 199 PHE 0.016 0.002 PHE E 34 TYR 0.012 0.002 TYR F 67 ARG 0.004 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 370) hydrogen bonds : angle 4.14774 ( 1236) covalent geometry : bond 0.00508 (10347) covalent geometry : angle 0.59031 (14097) *********************** 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 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.185 Fit side-chains REVERT: F 137 MET cc_start: 0.7487 (pmm) cc_final: 0.7245 (pmm) REVERT: T 8 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9094 (p) REVERT: T 69 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 23 PHE cc_start: 0.6982 (t80) cc_final: 0.6695 (t80) REVERT: C 23 PHE cc_start: 0.6953 (t80) cc_final: 0.6646 (t80) REVERT: D 23 PHE cc_start: 0.7125 (t80) cc_final: 0.6892 (t80) REVERT: E 23 PHE cc_start: 0.6898 (t80) cc_final: 0.6567 (t80) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.2566 time to fit residues: 56.4633 Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 A residue 19 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 138 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 18 THR 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 131 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.088656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.070712 restraints weight = 23416.376| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.60 r_work: 0.2889 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10347 Z= 0.172 Angle : 0.558 7.082 14097 Z= 0.313 Chirality : 0.046 0.168 1664 Planarity : 0.005 0.053 1857 Dihedral : 4.894 22.062 1447 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Rotamer: Outliers : 2.12 % Allowed : 13.10 % Favored : 84.78 % 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: -0.66 (0.22), residues: 1354 helix: 2.35 (0.34), residues: 253 sheet: -0.25 (0.24), residues: 481 loop : -1.83 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 199 PHE 0.014 0.002 PHE E 34 TYR 0.012 0.001 TYR F 67 ARG 0.003 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 370) hydrogen bonds : angle 4.04403 ( 1236) covalent geometry : bond 0.00408 (10347) covalent geometry : angle 0.55825 (14097) *********************** 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 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.356 Fit side-chains REVERT: A 23 PHE cc_start: 0.6984 (t80) cc_final: 0.6692 (t80) REVERT: C 23 PHE cc_start: 0.6907 (t80) cc_final: 0.6587 (t80) REVERT: D 23 PHE cc_start: 0.7095 (t80) cc_final: 0.6860 (t80) REVERT: E 23 PHE cc_start: 0.6899 (t80) cc_final: 0.6521 (t80) outliers start: 23 outliers final: 19 residues processed: 157 average time/residue: 0.2818 time to fit residues: 59.6271 Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A 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 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 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 12 optimal weight: 50.0000 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073987 restraints weight = 23297.210| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.63 r_work: 0.2960 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10347 Z= 0.106 Angle : 0.508 7.160 14097 Z= 0.279 Chirality : 0.045 0.221 1664 Planarity : 0.004 0.048 1857 Dihedral : 4.347 19.036 1447 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Rotamer: Outliers : 1.57 % Allowed : 13.75 % Favored : 84.69 % 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: -0.60 (0.22), residues: 1354 helix: 2.50 (0.34), residues: 252 sheet: -0.23 (0.24), residues: 475 loop : -1.81 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 199 PHE 0.010 0.001 PHE T 133 TYR 0.012 0.001 TYR F 360 ARG 0.011 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 370) hydrogen bonds : angle 3.83473 ( 1236) covalent geometry : bond 0.00219 (10347) covalent geometry : angle 0.50765 (14097) *********************** 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 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.237 Fit side-chains REVERT: F 179 THR cc_start: 0.8238 (m) cc_final: 0.7930 (t) REVERT: T 8 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9009 (p) REVERT: T 125 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.4169 (mmt180) REVERT: A 23 PHE cc_start: 0.6837 (t80) cc_final: 0.6537 (t80) REVERT: C 23 PHE cc_start: 0.6812 (t80) cc_final: 0.6481 (t80) REVERT: D 23 PHE cc_start: 0.7062 (t80) cc_final: 0.6808 (t80) REVERT: E 23 PHE cc_start: 0.6876 (t80) cc_final: 0.6498 (t80) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 0.3652 time to fit residues: 76.5066 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 8 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain A 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 19 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.090086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072096 restraints weight = 23397.456| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.62 r_work: 0.2922 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1851 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= 0.142 Angle : 0.530 7.509 14097 Z= 0.294 Chirality : 0.045 0.226 1664 Planarity : 0.005 0.050 1857 Dihedral : 4.534 26.038 1447 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 1.94 % Allowed : 13.93 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1354 helix: 2.53 (0.34), residues: 253 sheet: -0.19 (0.24), residues: 475 loop : -1.81 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 PHE 0.020 0.002 PHE T 23 TYR 0.012 0.001 TYR F 67 ARG 0.005 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 370) hydrogen bonds : angle 3.82347 ( 1236) covalent geometry : bond 0.00328 (10347) covalent geometry : angle 0.52998 (14097) ********************** 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 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.913 Fit side-chains REVERT: T 8 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9025 (p) REVERT: T 125 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4155 (mmt180) REVERT: A 23 PHE cc_start: 0.6936 (t80) cc_final: 0.6616 (t80) REVERT: C 23 PHE cc_start: 0.6871 (t80) cc_final: 0.6545 (t80) REVERT: D 23 PHE cc_start: 0.7127 (t80) cc_final: 0.6889 (t80) REVERT: E 23 PHE cc_start: 0.6896 (t80) cc_final: 0.6529 (t80) REVERT: E 125 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.3226 (mmt180) outliers start: 21 outliers final: 15 residues processed: 150 average time/residue: 0.3393 time to fit residues: 68.5929 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 80 SER 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 18 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain A 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 C residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 125 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 121 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.089063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071082 restraints weight = 23247.552| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.61 r_work: 0.2899 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10347 Z= 0.167 Angle : 0.564 7.606 14097 Z= 0.315 Chirality : 0.046 0.230 1664 Planarity : 0.005 0.052 1857 Dihedral : 4.726 24.082 1447 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 2.03 % Allowed : 13.93 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1354 helix: 2.47 (0.34), residues: 253 sheet: -0.19 (0.24), residues: 481 loop : -1.80 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 199 PHE 0.014 0.002 PHE T 23 TYR 0.012 0.001 TYR F 67 ARG 0.005 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 370) hydrogen bonds : angle 3.89761 ( 1236) covalent geometry : bond 0.00393 (10347) covalent geometry : angle 0.56377 (14097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6080.40 seconds wall clock time: 108 minutes 54.93 seconds (6534.93 seconds total)