Starting phenix.real_space_refine on Wed Aug 5 10:10:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.map" model { file = "/net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh1_53954/08_2026/9rh1_53954.cif" } resolution = 2.7 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 38 5.16 5 C 6012 2.51 5 N 1482 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9218 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2833 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 15, 'TRANS': 363} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2833 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 15, 'TRANS': 363} Chain: "E" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9218 At special positions: 0 Unit cell: (89.559, 123.039, 103.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 3 15.00 O 1683 8.00 N 1482 7.00 C 6012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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: 0.70 Conformation dependent library (CDL) restraints added in 255.0 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 15 sheets defined 53.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.603A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.783A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.922A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.549A pdb=" N GLU A 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.547A pdb=" N ALA A 131 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.622A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.817A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.589A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.982A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 12 through 31 Processing helix chain 'D' and resid 31 through 43 removed outlier: 4.601A pdb=" N GLY D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 85 removed outlier: 3.536A pdb=" N MET D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 117 removed outlier: 4.934A pdb=" N PHE D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Proline residue: D 97 - end of helix Proline residue: D 108 - end of helix removed outlier: 3.878A pdb=" N PHE D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.533A pdb=" N GLU D 124 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.534A pdb=" N ALA D 131 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 149 through 175 Processing helix chain 'D' and resid 180 through 200 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.627A pdb=" N TYR D 208 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 237 removed outlier: 3.787A pdb=" N GLY D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 262 Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 298 through 314 Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 338 through 351 Processing helix chain 'D' and resid 354 through 384 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.503A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.544A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.164A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 45 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.722A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.829A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.829A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.540A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.234A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 45 " --> pdb=" O THR E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.773A pdb=" N CYS E 96 " --> pdb=" O TRP E 108 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP E 108 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS E 98 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.795A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.655A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1662 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: 1.57 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1507 1.32 - 1.45: 2451 1.45 - 1.57: 5390 1.57 - 1.69: 6 1.69 - 1.82: 62 Bond restraints: 9416 Sorted by residual: bond pdb=" OB5 CDL A 501 " pdb=" PB2 CDL A 501 " ideal model delta sigma weight residual 1.657 1.572 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" OA5 CDL A 501 " pdb=" PA1 CDL A 501 " ideal model delta sigma weight residual 1.651 1.579 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" OA2 CDL A 501 " pdb=" PA1 CDL A 501 " ideal model delta sigma weight residual 1.639 1.578 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" OB2 CDL A 501 " pdb=" PB2 CDL A 501 " ideal model delta sigma weight residual 1.636 1.576 0.060 2.00e-02 2.50e+03 8.92e+00 bond pdb=" CB3 CDL A 501 " pdb=" OB5 CDL A 501 " ideal model delta sigma weight residual 1.403 1.442 -0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 9411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 12629 2.59 - 5.17: 140 5.17 - 7.76: 20 7.76 - 10.34: 2 10.34 - 12.93: 1 Bond angle restraints: 12792 Sorted by residual: angle pdb=" CA LEU F 11 " pdb=" CB LEU F 11 " pdb=" CG LEU F 11 " ideal model delta sigma weight residual 116.30 129.23 -12.93 3.50e+00 8.16e-02 1.36e+01 angle pdb=" C ASP E 104 " pdb=" CA ASP E 104 " pdb=" CB ASP E 104 " ideal model delta sigma weight residual 115.89 111.39 4.50 1.32e+00 5.74e-01 1.16e+01 angle pdb=" N ARG D 313 " pdb=" CA ARG D 313 " pdb=" CB ARG D 313 " ideal model delta sigma weight residual 110.12 114.83 -4.71 1.47e+00 4.63e-01 1.03e+01 angle pdb=" CA ARG D 313 " pdb=" CB ARG D 313 " pdb=" CG ARG D 313 " ideal model delta sigma weight residual 114.10 108.37 5.73 2.00e+00 2.50e-01 8.22e+00 angle pdb=" CA THR F 7 " pdb=" CB THR F 7 " pdb=" CG2 THR F 7 " ideal model delta sigma weight residual 110.50 115.15 -4.65 1.70e+00 3.46e-01 7.47e+00 ... (remaining 12787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4929 16.99 - 33.98: 444 33.98 - 50.97: 140 50.97 - 67.96: 34 67.96 - 84.95: 7 Dihedral angle restraints: 5554 sinusoidal: 2120 harmonic: 3434 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.74 35.26 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.04 33.96 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 5551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1206 0.051 - 0.102: 248 0.102 - 0.153: 46 0.153 - 0.204: 4 0.204 - 0.255: 4 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR F 7 " pdb=" N THR F 7 " pdb=" C THR F 7 " pdb=" CB THR F 7 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB THR F 7 " pdb=" CA THR F 7 " pdb=" OG1 THR F 7 " pdb=" CG2 THR F 7 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1505 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 7 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO C 8 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 7 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO F 8 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " -0.203 9.50e-02 1.11e+02 9.10e-02 5.10e+00 pdb=" NE ARG D 313 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " -0.007 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2022 2.79 - 3.31: 8731 3.31 - 3.84: 15491 3.84 - 4.37: 18289 4.37 - 4.90: 31651 Nonbonded interactions: 76184 Sorted by model distance: nonbonded pdb=" NZ LYS A 57 " pdb=" OD2 ASP A 65 " model vdw 2.258 3.120 nonbonded pdb=" NZ LYS D 57 " pdb=" OD2 ASP D 65 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR D 38 " pdb=" O PHE D 269 " model vdw 2.302 3.040 nonbonded pdb=" O SER F 69 " pdb=" OG SER F 69 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP B 104 " pdb=" OG SER C 34 " model vdw 2.310 3.040 ... (remaining 76179 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' and resid 10 through 388) selection = (chain 'D' and resid 10 through 388) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.180 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.110 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 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 0.085 9420 Z= 0.172 Angle : 0.683 12.928 12800 Z= 0.331 Chirality : 0.044 0.255 1508 Planarity : 0.006 0.108 1566 Dihedral : 15.035 84.954 3354 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 17.18 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.31 (0.24), residues: 1194 helix: 1.52 (0.21), residues: 558 sheet: 1.32 (0.35), residues: 222 loop : -0.22 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 66 TYR 0.013 0.002 TYR C 49 PHE 0.021 0.001 PHE B 64 TRP 0.021 0.002 TRP C 35 HIS 0.014 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9416) covalent geometry : angle 0.68264 / 0.33 (12792) SS BOND : bond 0.00309 / 0.15 ( 4) SS BOND : angle 0.81541 / 0.43 ( 8) hydrogen bonds : bond 0.21793 / 14.53 ( 577) hydrogen bonds : angle 7.22824 / 5.13 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: D 321 GLU cc_start: 0.7609 (tt0) cc_final: 0.7388 (tt0) REVERT: E 107 TYR cc_start: 0.7421 (m-10) cc_final: 0.7138 (m-10) REVERT: F 56 SER cc_start: 0.7914 (m) cc_final: 0.7542 (p) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.6226 time to fit residues: 94.6892 Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 58 ASN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 38 GLN E 43 HIS F 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086564 restraints weight = 11201.808| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.35 r_work: 0.2786 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9420 Z= 0.242 Angle : 0.670 6.822 12800 Z= 0.341 Chirality : 0.044 0.168 1508 Planarity : 0.004 0.035 1566 Dihedral : 8.475 61.826 1382 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.31 % Allowed : 15.11 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.75 (0.24), residues: 1194 helix: 1.91 (0.21), residues: 572 sheet: 1.72 (0.35), residues: 210 loop : -0.17 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.017 0.002 TYR C 49 PHE 0.019 0.002 PHE D 72 TRP 0.011 0.002 TRP F 35 HIS 0.006 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.24 ( 9416) covalent geometry : angle 0.66988 / 0.34 (12792) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 0.69664 / 0.35 ( 8) hydrogen bonds : bond 0.05113 / 3.40 ( 577) hydrogen bonds : angle 5.23919 / 3.78 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.369 Fit side-chains REVERT: A 345 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8984 (mm) REVERT: B 5 HIS cc_start: 0.6020 (OUTLIER) cc_final: 0.5796 (t-90) REVERT: E 107 TYR cc_start: 0.7353 (m-80) cc_final: 0.7095 (m-10) REVERT: F 39 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4898 (pptt) outliers start: 32 outliers final: 13 residues processed: 161 average time/residue: 0.5747 time to fit residues: 98.8348 Evaluate side-chains 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 43 HIS D 56 ASN E 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.159588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091348 restraints weight = 11133.138| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.38 r_work: 0.2838 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9420 Z= 0.105 Angle : 0.549 6.856 12800 Z= 0.279 Chirality : 0.039 0.162 1508 Planarity : 0.003 0.029 1566 Dihedral : 8.116 58.602 1382 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.80 % Allowed : 15.94 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.08 (0.24), residues: 1194 helix: 2.29 (0.21), residues: 560 sheet: 1.77 (0.35), residues: 210 loop : -0.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE A 136 TRP 0.011 0.001 TRP A 216 HIS 0.007 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9416) covalent geometry : angle 0.54939 / 0.28 (12792) SS BOND : bond 0.00356 / 0.18 ( 4) SS BOND : angle 0.54058 / 0.29 ( 8) hydrogen bonds : bond 0.03808 / 2.53 ( 577) hydrogen bonds : angle 4.84099 / 3.50 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.360 Fit side-chains REVERT: A 181 MET cc_start: 0.8494 (mmt) cc_final: 0.8267 (mmm) REVERT: C 65 SER cc_start: 0.6794 (OUTLIER) cc_final: 0.6463 (p) REVERT: D 157 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8561 (tmm) REVERT: D 359 ASN cc_start: 0.8203 (t0) cc_final: 0.7725 (m-40) REVERT: E 34 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7207 (mmt) REVERT: E 74 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6645 (mttp) REVERT: E 107 TYR cc_start: 0.7241 (m-80) cc_final: 0.6994 (m-10) REVERT: F 45 LYS cc_start: 0.7213 (ttmm) cc_final: 0.6690 (ttpp) REVERT: F 61 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7039 (mtp180) outliers start: 27 outliers final: 10 residues processed: 158 average time/residue: 0.5925 time to fit residues: 99.8448 Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 103 optimal weight: 20.0000 chunk 13 optimal weight: 0.3980 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091335 restraints weight = 11225.211| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.38 r_work: 0.2862 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9420 Z= 0.107 Angle : 0.528 6.099 12800 Z= 0.268 Chirality : 0.039 0.152 1508 Planarity : 0.003 0.032 1566 Dihedral : 7.945 58.678 1382 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.45 % Allowed : 15.32 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.90 (0.24), residues: 1194 helix: 2.11 (0.21), residues: 588 sheet: 1.90 (0.35), residues: 206 loop : -0.39 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.016 0.001 TYR C 91 PHE 0.015 0.001 PHE B 64 TRP 0.011 0.001 TRP B 36 HIS 0.006 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9416) covalent geometry : angle 0.52839 / 0.27 (12792) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 0.50696 / 0.27 ( 8) hydrogen bonds : bond 0.03664 / 2.42 ( 577) hydrogen bonds : angle 4.68444 / 3.39 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: A 243 HIS cc_start: 0.8264 (m-70) cc_final: 0.8006 (m90) REVERT: B 11 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5262 (mm) REVERT: C 65 SER cc_start: 0.6775 (OUTLIER) cc_final: 0.6446 (p) REVERT: D 150 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7706 (mp) REVERT: D 240 LYS cc_start: 0.6433 (mppt) cc_final: 0.6199 (mppt) REVERT: D 359 ASN cc_start: 0.8193 (t0) cc_final: 0.7745 (m-40) REVERT: E 74 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6716 (mttp) REVERT: E 107 TYR cc_start: 0.7292 (m-80) cc_final: 0.7072 (m-10) REVERT: F 45 LYS cc_start: 0.7203 (ttmm) cc_final: 0.6645 (ttpp) REVERT: F 61 ARG cc_start: 0.7251 (mtp180) cc_final: 0.7011 (mtp180) outliers start: 43 outliers final: 20 residues processed: 160 average time/residue: 0.6088 time to fit residues: 104.1150 Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088485 restraints weight = 11316.294| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.34 r_work: 0.2805 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9420 Z= 0.159 Angle : 0.569 6.934 12800 Z= 0.287 Chirality : 0.041 0.155 1508 Planarity : 0.004 0.034 1566 Dihedral : 8.012 55.684 1382 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.62 % Allowed : 16.36 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.77 (0.24), residues: 1194 helix: 2.04 (0.21), residues: 588 sheet: 1.67 (0.36), residues: 192 loop : -0.33 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.016 0.001 TYR C 49 PHE 0.015 0.001 PHE D 72 TRP 0.011 0.001 TRP E 36 HIS 0.005 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9416) covalent geometry : angle 0.56850 / 0.29 (12792) SS BOND : bond 0.00313 / 0.16 ( 4) SS BOND : angle 0.62063 / 0.34 ( 8) hydrogen bonds : bond 0.04215 / 2.78 ( 577) hydrogen bonds : angle 4.76271 / 3.46 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.383 Fit side-chains REVERT: A 243 HIS cc_start: 0.8291 (m-70) cc_final: 0.8080 (m90) REVERT: B 11 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5210 (mm) REVERT: C 12 SER cc_start: 0.5049 (t) cc_final: 0.4521 (p) REVERT: C 61 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6714 (mtm110) REVERT: D 157 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8812 (ttm) REVERT: D 315 LYS cc_start: 0.8992 (mptp) cc_final: 0.8708 (mppt) REVERT: E 107 TYR cc_start: 0.7420 (m-80) cc_final: 0.7220 (m-10) REVERT: F 45 LYS cc_start: 0.7189 (ttmm) cc_final: 0.6619 (ttpp) REVERT: F 61 ARG cc_start: 0.7305 (mtp180) cc_final: 0.7042 (mtp180) outliers start: 35 outliers final: 22 residues processed: 160 average time/residue: 0.6018 time to fit residues: 102.7730 Evaluate side-chains 157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088653 restraints weight = 11253.829| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.37 r_work: 0.2814 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9420 Z= 0.146 Angle : 0.557 11.129 12800 Z= 0.280 Chirality : 0.040 0.171 1508 Planarity : 0.004 0.035 1566 Dihedral : 7.926 55.147 1382 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.31 % Allowed : 16.87 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.93 (0.24), residues: 1194 helix: 2.19 (0.21), residues: 574 sheet: 1.71 (0.36), residues: 192 loop : -0.16 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.015 0.001 TYR C 91 PHE 0.014 0.001 PHE D 72 TRP 0.015 0.001 TRP B 36 HIS 0.005 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9416) covalent geometry : angle 0.55721 / 0.28 (12792) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 0.53139 / 0.29 ( 8) hydrogen bonds : bond 0.04005 / 2.64 ( 577) hydrogen bonds : angle 4.72203 / 3.43 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 56 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (m-40) REVERT: A 243 HIS cc_start: 0.8265 (m-70) cc_final: 0.8004 (m-70) REVERT: B 11 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5187 (mm) REVERT: C 12 SER cc_start: 0.4920 (t) cc_final: 0.4575 (p) REVERT: C 65 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6683 (p) REVERT: D 123 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8135 (ptp90) REVERT: D 157 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8766 (ttm) REVERT: D 366 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 45 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6526 (ttpp) REVERT: F 61 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6994 (mtp180) outliers start: 32 outliers final: 20 residues processed: 151 average time/residue: 0.6198 time to fit residues: 99.6536 Evaluate side-chains 151 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089873 restraints weight = 11268.934| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.38 r_work: 0.2805 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.117 Angle : 0.535 10.335 12800 Z= 0.268 Chirality : 0.039 0.149 1508 Planarity : 0.003 0.035 1566 Dihedral : 7.729 58.129 1382 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.42 % Allowed : 16.87 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.02 (0.24), residues: 1194 helix: 2.27 (0.21), residues: 574 sheet: 1.78 (0.36), residues: 192 loop : -0.14 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.015 0.001 TYR C 91 PHE 0.011 0.001 PHE D 72 TRP 0.017 0.001 TRP B 36 HIS 0.004 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9416) covalent geometry : angle 0.53527 / 0.27 (12792) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.47458 / 0.26 ( 8) hydrogen bonds : bond 0.03705 / 2.44 ( 577) hydrogen bonds : angle 4.64182 / 3.37 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8286 (m-70) cc_final: 0.8023 (m-70) REVERT: B 11 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5205 (mm) REVERT: C 12 SER cc_start: 0.4919 (t) cc_final: 0.4621 (p) REVERT: C 65 SER cc_start: 0.7017 (OUTLIER) cc_final: 0.6696 (p) REVERT: D 123 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (ptp90) REVERT: D 150 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (mp) REVERT: D 359 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7817 (m110) REVERT: F 45 LYS cc_start: 0.7052 (ttmm) cc_final: 0.6844 (ttpt) REVERT: F 61 ARG cc_start: 0.7279 (mtp180) cc_final: 0.7025 (mtp180) outliers start: 33 outliers final: 21 residues processed: 153 average time/residue: 0.6473 time to fit residues: 105.5073 Evaluate side-chains 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 102 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.090716 restraints weight = 11111.509| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.37 r_work: 0.2856 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.112 Angle : 0.525 10.112 12800 Z= 0.265 Chirality : 0.039 0.147 1508 Planarity : 0.003 0.034 1566 Dihedral : 7.592 59.523 1382 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.00 % Allowed : 17.91 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.07 (0.24), residues: 1194 helix: 2.32 (0.21), residues: 574 sheet: 1.75 (0.36), residues: 192 loop : -0.12 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.015 0.001 TYR C 91 PHE 0.012 0.001 PHE B 64 TRP 0.037 0.001 TRP B 36 HIS 0.004 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9416) covalent geometry : angle 0.52536 / 0.26 (12792) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 0.49662 / 0.27 ( 8) hydrogen bonds : bond 0.03626 / 2.39 ( 577) hydrogen bonds : angle 4.60678 / 3.34 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8297 (m-70) cc_final: 0.8030 (m-70) REVERT: B 11 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5229 (mm) REVERT: C 12 SER cc_start: 0.4947 (t) cc_final: 0.4682 (p) REVERT: C 65 SER cc_start: 0.6950 (OUTLIER) cc_final: 0.6636 (p) REVERT: D 123 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: D 150 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7671 (mp) REVERT: D 359 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7707 (m110) REVERT: F 61 ARG cc_start: 0.7255 (mtp180) cc_final: 0.7006 (mtp180) outliers start: 29 outliers final: 19 residues processed: 148 average time/residue: 0.6183 time to fit residues: 97.4628 Evaluate side-chains 151 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089913 restraints weight = 11075.635| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.38 r_work: 0.2845 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9420 Z= 0.126 Angle : 0.542 9.816 12800 Z= 0.271 Chirality : 0.039 0.149 1508 Planarity : 0.003 0.034 1566 Dihedral : 7.536 58.348 1382 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.69 % Allowed : 18.32 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.04 (0.24), residues: 1194 helix: 2.30 (0.21), residues: 574 sheet: 1.71 (0.36), residues: 194 loop : -0.14 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.016 0.001 TYR C 91 PHE 0.012 0.001 PHE D 72 TRP 0.030 0.001 TRP B 36 HIS 0.004 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9416) covalent geometry : angle 0.54163 / 0.27 (12792) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 0.54531 / 0.29 ( 8) hydrogen bonds : bond 0.03764 / 2.48 ( 577) hydrogen bonds : angle 4.58856 / 3.33 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8303 (m-70) cc_final: 0.8043 (m-70) REVERT: B 11 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5156 (mm) REVERT: C 12 SER cc_start: 0.4967 (t) cc_final: 0.4709 (p) REVERT: C 65 SER cc_start: 0.7071 (OUTLIER) cc_final: 0.6742 (p) REVERT: D 123 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8114 (ptp90) REVERT: D 150 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7741 (mp) REVERT: D 242 LYS cc_start: 0.8183 (tttm) cc_final: 0.7895 (tttm) REVERT: D 359 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7724 (m110) REVERT: F 61 ARG cc_start: 0.7248 (mtp180) cc_final: 0.7002 (mtp180) outliers start: 26 outliers final: 20 residues processed: 145 average time/residue: 0.6011 time to fit residues: 92.5722 Evaluate side-chains 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 69 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087825 restraints weight = 11080.515| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.40 r_work: 0.2796 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9420 Z= 0.171 Angle : 0.577 9.497 12800 Z= 0.289 Chirality : 0.041 0.154 1508 Planarity : 0.004 0.033 1566 Dihedral : 7.714 59.285 1382 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 18.01 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.94 (0.24), residues: 1194 helix: 2.20 (0.21), residues: 574 sheet: 1.76 (0.36), residues: 194 loop : -0.21 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.017 0.002 TYR C 91 PHE 0.015 0.001 PHE D 72 TRP 0.025 0.001 TRP B 36 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 9416) covalent geometry : angle 0.57730 / 0.29 (12792) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.54762 / 0.30 ( 8) hydrogen bonds : bond 0.04209 / 2.78 ( 577) hydrogen bonds : angle 4.69982 / 3.41 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8289 (m-70) cc_final: 0.8031 (m-70) REVERT: B 11 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5168 (mm) REVERT: C 12 SER cc_start: 0.4994 (t) cc_final: 0.4757 (p) REVERT: D 123 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: E 81 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.4324 (tpp) REVERT: F 61 ARG cc_start: 0.7278 (mtp180) cc_final: 0.7006 (mtp180) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.5736 time to fit residues: 91.4721 Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 40.0000 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091378 restraints weight = 11023.090| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.35 r_work: 0.2844 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9420 Z= 0.100 Angle : 0.535 9.735 12800 Z= 0.265 Chirality : 0.039 0.149 1508 Planarity : 0.003 0.033 1566 Dihedral : 7.384 57.397 1382 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.07 % Allowed : 18.84 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.08 (0.24), residues: 1194 helix: 2.33 (0.21), residues: 574 sheet: 1.82 (0.36), residues: 194 loop : -0.15 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.017 0.001 TYR C 91 PHE 0.008 0.001 PHE F 98 TRP 0.036 0.001 TRP B 36 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9416) covalent geometry : angle 0.53451 / 0.27 (12792) SS BOND : bond 0.00278 / 0.14 ( 4) SS BOND : angle 0.52938 / 0.28 ( 8) hydrogen bonds : bond 0.03476 / 2.30 ( 577) hydrogen bonds : angle 4.54825 / 3.30 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.66 seconds wall clock time: 68 minutes 21.68 seconds (4101.68 seconds total)