Starting phenix.real_space_refine on Wed Feb 4 14:37:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zor_60316/02_2026/8zor_60316_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zor_60316/02_2026/8zor_60316.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/8zor_60316/02_2026/8zor_60316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zor_60316/02_2026/8zor_60316.map" model { file = "/net/cci-nas-00/data/ceres_data/8zor_60316/02_2026/8zor_60316_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zor_60316/02_2026/8zor_60316_trim.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= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2046 atoms to isotropic. 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 54 5.16 5 C 6189 2.51 5 N 1488 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2432 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain breaks: 1 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2432 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain breaks: 1 Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "G" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2432 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain breaks: 1 Chain: "H" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9426 At special positions: 0 Unit cell: (98.44, 101.65, 86.67, 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 54 16.00 O 1695 8.00 N 1488 7.00 C 6189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 110 " distance=2.03 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 368.3 milliseconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 1 sheets defined 72.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 17 through 33 removed outlier: 4.071A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 58 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 70 through 91 removed outlier: 3.602A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 removed outlier: 3.579A pdb=" N LEU A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.263A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 removed outlier: 4.494A pdb=" N PHE A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.620A pdb=" N ILE A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.536A pdb=" N ILE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 306 removed outlier: 4.041A pdb=" N VAL A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.626A pdb=" N TYR A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.983A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.544A pdb=" N ALA A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.535A pdb=" N ALA D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 84 removed outlier: 4.169A pdb=" N LYS D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 17 through 33 removed outlier: 3.999A pdb=" N LEU C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 60 Processing helix chain 'C' and resid 66 through 91 removed outlier: 3.631A pdb=" N MET C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Proline residue: C 73 - end of helix removed outlier: 3.594A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 removed outlier: 3.526A pdb=" N LEU C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 133 through 138 removed outlier: 4.260A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 163 Proline residue: C 146 - end of helix removed outlier: 3.603A pdb=" N ARG C 162 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.890A pdb=" N GLY C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.647A pdb=" N ILE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C 268 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY C 271 " --> pdb=" O TRP C 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 278 through 306 removed outlier: 3.892A pdb=" N VAL C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.955A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.523A pdb=" N ALA C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'E' and resid 16 through 27 removed outlier: 3.547A pdb=" N ALA E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 22 " --> pdb=" O LYS E 18 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 84 removed outlier: 4.205A pdb=" N LYS E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.845A pdb=" N THR G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 33 removed outlier: 3.997A pdb=" N LEU G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 58 Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'G' and resid 71 through 91 removed outlier: 3.592A pdb=" N VAL G 85 " --> pdb=" O GLY G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 95 removed outlier: 3.841A pdb=" N LEU G 95 " --> pdb=" O LEU G 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 95' Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 114 through 128 Processing helix chain 'G' and resid 133 through 138 removed outlier: 4.191A pdb=" N GLY G 137 " --> pdb=" O ALA G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 162 Proline residue: G 146 - end of helix Processing helix chain 'G' and resid 211 through 220 Processing helix chain 'G' and resid 224 through 237 Processing helix chain 'G' and resid 239 through 247 removed outlier: 3.890A pdb=" N GLY G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 273 removed outlier: 3.581A pdb=" N ILE G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP G 267 " --> pdb=" O GLY G 263 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER G 268 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY G 271 " --> pdb=" O TRP G 267 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 276 No H-bonds generated for 'chain 'G' and resid 274 through 276' Processing helix chain 'G' and resid 278 through 306 removed outlier: 3.797A pdb=" N VAL G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) Proline residue: G 288 - end of helix Processing helix chain 'G' and resid 311 through 322 removed outlier: 4.188A pdb=" N VAL G 315 " --> pdb=" O GLY G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 336 Processing helix chain 'G' and resid 351 through 359 Processing helix chain 'G' and resid 360 through 370 Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.659A pdb=" N ALA H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS H 22 " --> pdb=" O LYS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 removed outlier: 4.269A pdb=" N LYS H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 13 current: chain 'D' and resid 59 through 66 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 66 current: chain 'E' and resid 59 through 66 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 66 current: chain 'H' and resid 59 through 66 No H-bonds generated for sheet with id=AA1 581 hydrogen bonds defined for protein. 1719 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: 1.40 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1494 1.29 - 1.42: 2276 1.42 - 1.55: 5735 1.55 - 1.68: 2 1.68 - 1.81: 96 Bond restraints: 9603 Sorted by residual: bond pdb=" C TYR A 140 " pdb=" O TYR A 140 " ideal model delta sigma weight residual 1.244 1.164 0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C TYR C 140 " pdb=" O TYR C 140 " ideal model delta sigma weight residual 1.244 1.171 0.072 9.40e-03 1.13e+04 5.94e+01 bond pdb=" C SER A 114 " pdb=" O SER A 114 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.21e-02 6.83e+03 3.17e+01 bond pdb=" C GLY A 115 " pdb=" O GLY A 115 " ideal model delta sigma weight residual 1.235 1.176 0.059 1.18e-02 7.18e+03 2.48e+01 bond pdb=" CA SER A 114 " pdb=" CB SER A 114 " ideal model delta sigma weight residual 1.530 1.459 0.070 1.43e-02 4.89e+03 2.41e+01 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12815 1.85 - 3.70: 162 3.70 - 5.55: 54 5.55 - 7.40: 6 7.40 - 9.25: 4 Bond angle restraints: 13041 Sorted by residual: angle pdb=" C ILE G 326 " pdb=" CA ILE G 326 " pdb=" CB ILE G 326 " ideal model delta sigma weight residual 111.71 107.11 4.60 8.50e-01 1.38e+00 2.93e+01 angle pdb=" CA ILE G 326 " pdb=" C ILE G 326 " pdb=" O ILE G 326 " ideal model delta sigma weight residual 120.70 116.93 3.77 8.50e-01 1.38e+00 1.97e+01 angle pdb=" CA TYR A 140 " pdb=" C TYR A 140 " pdb=" N PRO A 141 " ideal model delta sigma weight residual 120.81 124.59 -3.78 8.60e-01 1.35e+00 1.94e+01 angle pdb=" O VAL A 113 " pdb=" C VAL A 113 " pdb=" N SER A 114 " ideal model delta sigma weight residual 123.03 127.62 -4.59 1.05e+00 9.07e-01 1.91e+01 angle pdb=" CA TYR C 140 " pdb=" C TYR C 140 " pdb=" N PRO C 141 " ideal model delta sigma weight residual 120.52 123.81 -3.29 8.30e-01 1.45e+00 1.57e+01 ... (remaining 13036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 4957 17.04 - 34.08: 573 34.08 - 51.11: 129 51.11 - 68.15: 6 68.15 - 85.19: 8 Dihedral angle restraints: 5673 sinusoidal: 2106 harmonic: 3567 Sorted by residual: dihedral pdb=" N SER A 114 " pdb=" C SER A 114 " pdb=" CA SER A 114 " pdb=" CB SER A 114 " ideal model delta harmonic sigma weight residual 122.80 113.53 9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C SER A 114 " pdb=" N SER A 114 " pdb=" CA SER A 114 " pdb=" CB SER A 114 " ideal model delta harmonic sigma weight residual -122.60 -114.47 -8.13 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU G 127 " pdb=" CG GLU G 127 " pdb=" CD GLU G 127 " pdb=" OE1 GLU G 127 " ideal model delta sinusoidal sigma weight residual 0.00 -85.19 85.19 1 3.00e+01 1.11e-03 9.77e+00 ... (remaining 5670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1123 0.041 - 0.082: 367 0.082 - 0.123: 94 0.123 - 0.164: 7 0.164 - 0.205: 2 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA TYR A 140 " pdb=" N TYR A 140 " pdb=" C TYR A 140 " pdb=" CB TYR A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA SER A 114 " pdb=" N SER A 114 " pdb=" C SER A 114 " pdb=" CB SER A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL G 113 " pdb=" N VAL G 113 " pdb=" C VAL G 113 " pdb=" CB VAL G 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1590 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 140 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C TYR C 140 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR C 140 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO C 141 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 340 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO G 341 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO G 341 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 341 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 113 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C VAL A 113 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 113 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 114 " 0.014 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 107 2.65 - 3.21: 8931 3.21 - 3.78: 14453 3.78 - 4.34: 20598 4.34 - 4.90: 34167 Nonbonded interactions: 78256 Sorted by model distance: nonbonded pdb=" OH TYR G 140 " pdb=" O3 BCT G 401 " model vdw 2.091 3.040 nonbonded pdb=" OD1 ASP E 77 " pdb=" OH TYR H 100 " model vdw 2.132 3.040 nonbonded pdb=" OG SER E 27 " pdb=" OE1 GLU E 74 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP G 325 " pdb=" OG1 THR G 353 " model vdw 2.226 3.040 nonbonded pdb=" O PRO G 146 " pdb=" OG1 THR G 150 " model vdw 2.246 3.040 ... (remaining 78251 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9606 Z= 0.233 Angle : 0.573 9.247 13047 Z= 0.306 Chirality : 0.042 0.205 1593 Planarity : 0.005 0.063 1602 Dihedral : 14.533 85.190 3390 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.20 % Allowed : 17.58 % Favored : 82.22 % 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 are not related in a simple way. whole: -1.26 (0.23), residues: 1239 helix: -0.57 (0.17), residues: 867 sheet: -0.95 (0.51), residues: 99 loop : -1.03 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 333 TYR 0.025 0.001 TYR C 140 PHE 0.006 0.001 PHE A 110 TRP 0.006 0.001 TRP A 212 HIS 0.001 0.000 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9603) covalent geometry : angle 0.57337 (13041) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.33747 ( 6) hydrogen bonds : bond 0.24750 ( 581) hydrogen bonds : angle 8.06901 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.369 Fit side-chains REVERT: A 140 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7776 (t80) outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.0867 time to fit residues: 18.7877 Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain C residue 276 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.112200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.088539 restraints weight = 11993.484| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.07 r_work: 0.2780 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9606 Z= 0.154 Angle : 0.596 8.247 13047 Z= 0.296 Chirality : 0.044 0.125 1593 Planarity : 0.005 0.051 1602 Dihedral : 3.756 20.256 1326 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.92 % Allowed : 16.06 % Favored : 82.02 % 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 are not related in a simple way. whole: -0.23 (0.24), residues: 1239 helix: 0.48 (0.18), residues: 855 sheet: -1.18 (0.51), residues: 99 loop : -1.41 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 69 TYR 0.013 0.001 TYR A 344 PHE 0.012 0.001 PHE C 86 TRP 0.008 0.001 TRP G 212 HIS 0.001 0.000 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9603) covalent geometry : angle 0.59657 (13041) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.33369 ( 6) hydrogen bonds : bond 0.04975 ( 581) hydrogen bonds : angle 4.61720 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.359 Fit side-chains REVERT: A 104 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 250 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7678 (pp) REVERT: D 26 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 300 MET cc_start: 0.8298 (mmm) cc_final: 0.7980 (mmm) REVERT: C 319 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7333 (tt) REVERT: E 26 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7809 (mt-10) REVERT: G 104 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7936 (mm) REVERT: H 100 TYR cc_start: 0.8255 (m-80) cc_final: 0.7594 (m-10) outliers start: 19 outliers final: 11 residues processed: 175 average time/residue: 0.0942 time to fit residues: 23.9039 Evaluate side-chains 163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 0.0020 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.114885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.091279 restraints weight = 12005.451| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.06 r_work: 0.3165 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9606 Z= 0.122 Angle : 0.533 7.434 13047 Z= 0.261 Chirality : 0.042 0.124 1593 Planarity : 0.004 0.051 1602 Dihedral : 3.581 19.891 1324 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.42 % Allowed : 16.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1239 helix: 0.86 (0.18), residues: 852 sheet: -1.35 (0.49), residues: 99 loop : -1.39 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 69 TYR 0.012 0.001 TYR A 140 PHE 0.006 0.001 PHE A 86 TRP 0.005 0.001 TRP A 267 HIS 0.001 0.000 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9603) covalent geometry : angle 0.53337 (13041) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.23482 ( 6) hydrogen bonds : bond 0.04323 ( 581) hydrogen bonds : angle 4.19000 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.239 Fit side-chains REVERT: A 217 GLU cc_start: 0.8112 (tp30) cc_final: 0.7803 (tt0) REVERT: A 229 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 250 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7601 (pp) REVERT: D 26 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 229 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7363 (tp) REVERT: C 300 MET cc_start: 0.8164 (mmm) cc_final: 0.7792 (mmm) REVERT: E 26 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7804 (mt-10) REVERT: G 104 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7915 (mm) REVERT: G 300 MET cc_start: 0.8162 (mmm) cc_final: 0.7838 (mmm) outliers start: 24 outliers final: 13 residues processed: 180 average time/residue: 0.0861 time to fit residues: 22.4479 Evaluate side-chains 167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 0.0570 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.092412 restraints weight = 12083.846| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.09 r_work: 0.3156 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9606 Z= 0.115 Angle : 0.526 7.307 13047 Z= 0.256 Chirality : 0.041 0.123 1593 Planarity : 0.004 0.050 1602 Dihedral : 3.527 19.953 1324 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 16.97 % Favored : 80.20 % 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 are not related in a simple way. whole: 0.36 (0.25), residues: 1239 helix: 1.00 (0.19), residues: 855 sheet: -1.43 (0.49), residues: 99 loop : -1.27 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.013 0.001 TYR G 344 PHE 0.006 0.001 PHE C 86 TRP 0.005 0.001 TRP A 267 HIS 0.002 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9603) covalent geometry : angle 0.52598 (13041) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.21600 ( 6) hydrogen bonds : bond 0.03906 ( 581) hydrogen bonds : angle 4.03216 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.274 Fit side-chains REVERT: A 104 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7901 (mm) REVERT: A 217 GLU cc_start: 0.8094 (tp30) cc_final: 0.7796 (tt0) REVERT: A 219 LEU cc_start: 0.8312 (tp) cc_final: 0.8101 (tp) REVERT: A 229 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7433 (tp) REVERT: A 250 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7576 (pp) REVERT: D 26 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 77 ASP cc_start: 0.7782 (m-30) cc_final: 0.7581 (m-30) REVERT: C 229 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7300 (tp) REVERT: C 300 MET cc_start: 0.8185 (mmm) cc_final: 0.7734 (mmm) REVERT: C 319 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7326 (tt) REVERT: E 26 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 104 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7897 (mm) REVERT: H 100 TYR cc_start: 0.8287 (m-80) cc_final: 0.7712 (m-80) outliers start: 28 outliers final: 13 residues processed: 178 average time/residue: 0.0799 time to fit residues: 20.7817 Evaluate side-chains 170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093446 restraints weight = 12017.752| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.04 r_work: 0.2835 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9606 Z= 0.110 Angle : 0.513 6.565 13047 Z= 0.251 Chirality : 0.041 0.123 1593 Planarity : 0.004 0.048 1602 Dihedral : 3.499 20.139 1324 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.74 % Allowed : 16.97 % Favored : 79.29 % 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 are not related in a simple way. whole: 0.46 (0.25), residues: 1239 helix: 1.07 (0.19), residues: 858 sheet: -1.46 (0.49), residues: 99 loop : -1.23 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.013 0.001 TYR A 140 PHE 0.005 0.001 PHE A 86 TRP 0.005 0.001 TRP A 267 HIS 0.003 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9603) covalent geometry : angle 0.51262 (13041) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.18596 ( 6) hydrogen bonds : bond 0.03729 ( 581) hydrogen bonds : angle 3.95420 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.334 Fit side-chains REVERT: A 80 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7515 (mt) REVERT: A 104 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 229 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7234 (tp) REVERT: A 250 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7443 (pp) REVERT: D 26 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 80 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7372 (mt) REVERT: C 229 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7122 (tp) REVERT: C 319 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7305 (tt) REVERT: E 26 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7731 (mt-10) REVERT: G 95 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7869 (mm) REVERT: G 104 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7770 (mm) REVERT: G 250 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7626 (pp) REVERT: H 100 TYR cc_start: 0.8235 (m-80) cc_final: 0.7604 (m-80) outliers start: 37 outliers final: 20 residues processed: 190 average time/residue: 0.0800 time to fit residues: 22.3851 Evaluate side-chains 182 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.110813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087059 restraints weight = 12082.350| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.04 r_work: 0.2744 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9606 Z= 0.181 Angle : 0.581 7.811 13047 Z= 0.284 Chirality : 0.044 0.144 1593 Planarity : 0.005 0.054 1602 Dihedral : 3.693 17.891 1324 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.54 % Allowed : 17.17 % Favored : 79.29 % 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 are not related in a simple way. whole: 0.23 (0.24), residues: 1239 helix: 0.88 (0.18), residues: 864 sheet: -1.38 (0.50), residues: 99 loop : -1.38 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 69 TYR 0.016 0.001 TYR A 344 PHE 0.010 0.001 PHE A 110 TRP 0.006 0.001 TRP A 267 HIS 0.003 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9603) covalent geometry : angle 0.58080 (13041) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.46555 ( 6) hydrogen bonds : bond 0.04320 ( 581) hydrogen bonds : angle 4.09664 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.260 Fit side-chains REVERT: A 104 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 229 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7454 (tp) REVERT: A 250 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7763 (pp) REVERT: D 26 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 80 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7520 (mt) REVERT: C 229 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7346 (tp) REVERT: C 319 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7348 (tt) REVERT: E 26 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7755 (mt-10) REVERT: G 95 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8102 (mm) REVERT: G 104 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7832 (mm) REVERT: G 250 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7888 (pp) REVERT: H 100 TYR cc_start: 0.8336 (m-80) cc_final: 0.7885 (m-80) outliers start: 35 outliers final: 19 residues processed: 184 average time/residue: 0.0846 time to fit residues: 22.8412 Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.115433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.091901 restraints weight = 12025.756| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.03 r_work: 0.2823 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9606 Z= 0.113 Angle : 0.524 6.938 13047 Z= 0.256 Chirality : 0.042 0.137 1593 Planarity : 0.004 0.049 1602 Dihedral : 3.563 12.662 1323 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.79 % 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 are not related in a simple way. whole: 0.37 (0.25), residues: 1239 helix: 1.01 (0.19), residues: 864 sheet: -1.46 (0.49), residues: 99 loop : -1.33 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.013 0.001 TYR A 140 PHE 0.005 0.001 PHE G 86 TRP 0.005 0.001 TRP A 267 HIS 0.003 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9603) covalent geometry : angle 0.52386 (13041) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.20688 ( 6) hydrogen bonds : bond 0.03731 ( 581) hydrogen bonds : angle 3.96193 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.337 Fit side-chains REVERT: A 80 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7737 (mt) REVERT: A 104 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 217 GLU cc_start: 0.8149 (tp30) cc_final: 0.7853 (tt0) REVERT: A 229 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 250 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7539 (pp) REVERT: D 26 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 1 MET cc_start: 0.4876 (tmm) cc_final: 0.4599 (tmm) REVERT: C 80 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (mt) REVERT: C 229 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7286 (tp) REVERT: C 319 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (tt) REVERT: E 26 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7765 (mt-10) REVERT: G 95 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7966 (mm) REVERT: G 104 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7895 (mm) REVERT: G 250 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7811 (pp) REVERT: H 100 TYR cc_start: 0.8278 (m-80) cc_final: 0.7832 (m-80) outliers start: 35 outliers final: 21 residues processed: 186 average time/residue: 0.0697 time to fit residues: 19.3359 Evaluate side-chains 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 348 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.114923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.091374 restraints weight = 12003.884| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.05 r_work: 0.3148 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9606 Z= 0.117 Angle : 0.534 7.778 13047 Z= 0.258 Chirality : 0.042 0.153 1593 Planarity : 0.004 0.047 1602 Dihedral : 3.516 12.996 1323 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.64 % Allowed : 17.37 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1239 helix: 1.04 (0.19), residues: 864 sheet: -1.39 (0.50), residues: 99 loop : -1.35 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.013 0.001 TYR G 344 PHE 0.006 0.001 PHE C 86 TRP 0.005 0.001 TRP A 267 HIS 0.003 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9603) covalent geometry : angle 0.53416 (13041) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.23681 ( 6) hydrogen bonds : bond 0.03709 ( 581) hydrogen bonds : angle 3.95342 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.354 Fit side-chains REVERT: A 80 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7741 (mt) REVERT: A 104 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 217 GLU cc_start: 0.8206 (tp30) cc_final: 0.8002 (tt0) REVERT: A 229 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7457 (tp) REVERT: A 250 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7530 (pp) REVERT: C 1 MET cc_start: 0.4934 (tmm) cc_final: 0.4657 (tmm) REVERT: C 80 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 229 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7360 (tp) REVERT: C 319 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7387 (tt) REVERT: E 26 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7758 (mt-10) REVERT: G 95 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (mm) REVERT: G 104 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7905 (mm) REVERT: G 250 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7842 (pp) REVERT: H 100 TYR cc_start: 0.8282 (m-80) cc_final: 0.7891 (m-80) outliers start: 36 outliers final: 22 residues processed: 189 average time/residue: 0.0837 time to fit residues: 23.3817 Evaluate side-chains 183 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 348 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN G 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091391 restraints weight = 11975.125| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.06 r_work: 0.2838 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9606 Z= 0.125 Angle : 0.549 11.347 13047 Z= 0.264 Chirality : 0.042 0.135 1593 Planarity : 0.004 0.048 1602 Dihedral : 3.562 12.978 1323 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.64 % Allowed : 17.58 % Favored : 78.79 % 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 are not related in a simple way. whole: 0.43 (0.25), residues: 1239 helix: 1.03 (0.19), residues: 861 sheet: -1.34 (0.50), residues: 99 loop : -1.23 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.014 0.001 TYR G 344 PHE 0.006 0.001 PHE C 86 TRP 0.005 0.001 TRP A 267 HIS 0.003 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9603) covalent geometry : angle 0.54916 (13041) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.26899 ( 6) hydrogen bonds : bond 0.03753 ( 581) hydrogen bonds : angle 3.99462 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.336 Fit side-chains REVERT: A 80 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 104 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7993 (mm) REVERT: A 217 GLU cc_start: 0.8163 (tp30) cc_final: 0.7959 (tt0) REVERT: A 229 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 250 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7570 (pp) REVERT: C 1 MET cc_start: 0.4967 (tmm) cc_final: 0.4695 (tmm) REVERT: C 80 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7543 (mt) REVERT: C 229 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7385 (tp) REVERT: C 319 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7466 (tt) REVERT: E 26 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7782 (mt-10) REVERT: G 95 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8044 (mm) REVERT: G 104 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7991 (mm) REVERT: G 250 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7857 (pp) REVERT: H 26 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7923 (mt-10) REVERT: H 100 TYR cc_start: 0.8312 (m-80) cc_final: 0.7923 (m-80) outliers start: 36 outliers final: 23 residues processed: 186 average time/residue: 0.0778 time to fit residues: 21.4454 Evaluate side-chains 182 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 348 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.116031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.092652 restraints weight = 12039.241| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.04 r_work: 0.2816 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9606 Z= 0.109 Angle : 0.533 10.633 13047 Z= 0.256 Chirality : 0.041 0.148 1593 Planarity : 0.004 0.046 1602 Dihedral : 3.498 12.827 1323 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.23 % Allowed : 17.88 % Favored : 78.89 % 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 are not related in a simple way. whole: 0.54 (0.25), residues: 1239 helix: 1.14 (0.19), residues: 852 sheet: -1.32 (0.50), residues: 99 loop : -1.19 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 63 TYR 0.014 0.001 TYR A 140 PHE 0.005 0.001 PHE A 86 TRP 0.005 0.001 TRP C 267 HIS 0.005 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9603) covalent geometry : angle 0.53347 (13041) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.18895 ( 6) hydrogen bonds : bond 0.03557 ( 581) hydrogen bonds : angle 3.94781 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.351 Fit side-chains REVERT: A 80 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7623 (mt) REVERT: A 104 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 217 GLU cc_start: 0.8062 (tp30) cc_final: 0.7840 (tt0) REVERT: A 250 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7240 (pp) REVERT: C 1 MET cc_start: 0.4865 (tmm) cc_final: 0.4610 (tmm) REVERT: C 80 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7376 (mt) REVERT: C 229 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 319 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7288 (tt) REVERT: G 95 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (mm) REVERT: G 104 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7776 (mm) REVERT: G 250 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (pp) REVERT: H 26 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7988 (mt-10) REVERT: H 100 TYR cc_start: 0.8170 (m-80) cc_final: 0.7724 (m-80) outliers start: 32 outliers final: 19 residues processed: 180 average time/residue: 0.0802 time to fit residues: 21.3007 Evaluate side-chains 176 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 348 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 0.0060 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.115470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.092071 restraints weight = 11916.739| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.04 r_work: 0.3133 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9606 Z= 0.118 Angle : 0.539 8.628 13047 Z= 0.260 Chirality : 0.042 0.172 1593 Planarity : 0.004 0.047 1602 Dihedral : 3.520 12.926 1323 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 18.28 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1239 helix: 1.12 (0.19), residues: 852 sheet: -1.29 (0.50), residues: 99 loop : -1.26 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 89 TYR 0.014 0.001 TYR A 140 PHE 0.006 0.001 PHE A 86 TRP 0.005 0.001 TRP A 267 HIS 0.005 0.001 HIS G 303 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9603) covalent geometry : angle 0.53918 (13041) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.22408 ( 6) hydrogen bonds : bond 0.03636 ( 581) hydrogen bonds : angle 3.95781 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.78 seconds wall clock time: 37 minutes 38.26 seconds (2258.26 seconds total)