Starting phenix.real_space_refine on Sun Apr 5 12:41:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.map" model { file = "/net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ma5_63747/04_2026/9ma5_63747.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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 K 4 8.98 5 S 48 5.16 5 C 6608 2.51 5 N 1718 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10192 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 7, 'TRANS': 312} Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2484 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "C" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 7, 'TRANS': 312} Chain: "D" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2484 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 2, 'SPM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.24 Number of scatterers: 10192 At special positions: 0 Unit cell: (96.005, 90.73, 131.875, 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) K 4 19.00 S 48 16.00 O 1814 8.00 N 1718 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 140 " 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: 0.73 Conformation dependent library (CDL) restraints added in 543.1 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 23 sheets defined 35.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 68 through 100 removed outlier: 4.179A pdb=" N HIS A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 removed outlier: 3.648A pdb=" N ASN A 104 " --> pdb=" O ASP A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 143 through 174 removed outlier: 3.645A pdb=" N VAL A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.873A pdb=" N THR A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.760A pdb=" N TRP B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 94 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 140 through 171 removed outlier: 4.022A pdb=" N ARG B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 68 through 99 removed outlier: 4.171A pdb=" N HIS C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.549A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 104 " --> pdb=" O ASP C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 143 through 174 removed outlier: 3.584A pdb=" N VAL C 147 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.918A pdb=" N THR C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 63 through 94 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 140 through 171 removed outlier: 3.973A pdb=" N ARG D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.573A pdb=" N ALA D 325 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE D 315 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 212 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.573A pdb=" N ALA D 325 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE D 315 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU A 213 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR A 285 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.836A pdb=" N ALA A 188 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.497A pdb=" N TYR A 321 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU B 42 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 323 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.428A pdb=" N ALA B 185 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 235 through 237 removed outlier: 3.568A pdb=" N LEU B 249 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B 212 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASP B 245 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 237 removed outlier: 5.377A pdb=" N GLY B 210 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR B 286 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 222 removed outlier: 5.163A pdb=" N GLN B 219 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 231 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 46 removed outlier: 5.783A pdb=" N TYR B 323 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 315 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 212 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 46 removed outlier: 5.783A pdb=" N TYR B 323 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 315 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU C 213 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C 285 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 182 through 184 Processing sheet with id=AB6, first strand: chain 'C' and resid 182 through 184 Processing sheet with id=AB7, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AB8, first strand: chain 'C' and resid 314 through 316 removed outlier: 6.413A pdb=" N TYR C 321 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU D 42 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL C 323 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AC1, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.446A pdb=" N ALA D 185 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 235 through 237 removed outlier: 3.570A pdb=" N LEU D 249 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN D 212 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP D 245 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 235 through 237 removed outlier: 5.438A pdb=" N GLY D 210 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR D 286 " --> pdb=" O GLY D 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 219 through 222 removed outlier: 5.158A pdb=" N GLN D 219 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU D 231 " --> pdb=" O GLN D 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 309 through 311 508 hydrogen bonds defined for protein. 1479 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: 1.81 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3214 1.35 - 1.46: 2616 1.46 - 1.58: 4532 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10432 Sorted by residual: bond pdb=" CG LEU A 189 " pdb=" CD1 LEU A 189 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.87e+00 bond pdb=" N ARG C 33 " pdb=" CA ARG C 33 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.85e+00 bond pdb=" N ARG A 33 " pdb=" CA ARG A 33 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" CG LEU A 189 " pdb=" CD2 LEU A 189 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CG1 ILE D 148 " pdb=" CD1 ILE D 148 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.05e+00 ... (remaining 10427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14010 2.20 - 4.41: 127 4.41 - 6.61: 11 6.61 - 8.82: 2 8.82 - 11.02: 4 Bond angle restraints: 14154 Sorted by residual: angle pdb=" N VAL D 112 " pdb=" CA VAL D 112 " pdb=" C VAL D 112 " ideal model delta sigma weight residual 113.53 109.45 4.08 9.80e-01 1.04e+00 1.73e+01 angle pdb=" CB MET C 149 " pdb=" CG MET C 149 " pdb=" SD MET C 149 " ideal model delta sigma weight residual 112.70 123.72 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CB MET A 149 " pdb=" CG MET A 149 " pdb=" SD MET A 149 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C ALA C 32 " pdb=" N ARG C 33 " pdb=" CA ARG C 33 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C ALA A 32 " pdb=" N ARG A 33 " pdb=" CA ARG A 33 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.87e+00 ... (remaining 14149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5382 17.65 - 35.30: 578 35.30 - 52.95: 140 52.95 - 70.60: 46 70.60 - 88.25: 2 Dihedral angle restraints: 6148 sinusoidal: 2450 harmonic: 3698 Sorted by residual: dihedral pdb=" CA HIS A 49 " pdb=" C HIS A 49 " pdb=" N ILE A 50 " pdb=" CA ILE A 50 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA HIS C 49 " pdb=" C HIS C 49 " pdb=" N ILE C 50 " pdb=" CA ILE C 50 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA VAL B 109 " pdb=" C VAL B 109 " pdb=" N VAL B 110 " pdb=" CA VAL B 110 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1038 0.033 - 0.065: 390 0.065 - 0.098: 128 0.098 - 0.130: 69 0.130 - 0.163: 3 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CB ILE A 50 " pdb=" CA ILE A 50 " pdb=" CG1 ILE A 50 " pdb=" CG2 ILE A 50 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE C 50 " pdb=" CA ILE C 50 " pdb=" CG1 ILE C 50 " pdb=" CG2 ILE C 50 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1625 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 93 " 0.013 2.00e-02 2.50e+03 1.46e-02 5.33e+00 pdb=" CG TRP A 93 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 93 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 93 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 93 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 93 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 93 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 93 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 93 " 0.012 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP C 93 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 93 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 93 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 93 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 93 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 93 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 93 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 93 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 140 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO B 141 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.026 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.76: 1626 2.76 - 3.35: 11082 3.35 - 3.95: 19309 3.95 - 4.54: 26592 4.54 - 5.14: 42117 Nonbonded interactions: 100726 Sorted by model distance: nonbonded pdb=" O LEU C 126 " pdb=" OG1 THR C 130 " model vdw 2.164 3.040 nonbonded pdb=" O LEU D 123 " pdb=" OG1 THR D 127 " model vdw 2.166 3.040 nonbonded pdb=" O LEU A 126 " pdb=" OG1 THR A 130 " model vdw 2.166 3.040 nonbonded pdb=" O LEU B 123 " pdb=" OG1 THR B 127 " model vdw 2.176 3.040 nonbonded pdb=" O ALA C 32 " pdb=" OH TYR C 223 " model vdw 2.183 3.040 ... (remaining 100721 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 32 through 351) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 27 through 339) selection = (chain 'D' and resid 27 through 339) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.660 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10436 Z= 0.146 Angle : 0.552 11.021 14162 Z= 0.288 Chirality : 0.042 0.163 1628 Planarity : 0.004 0.046 1758 Dihedral : 15.949 88.254 3744 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.27 % Allowed : 22.00 % Favored : 77.73 % 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: 1.14 (0.24), residues: 1258 helix: 3.09 (0.23), residues: 408 sheet: -0.72 (0.32), residues: 266 loop : -0.16 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.013 0.001 TYR B 256 PHE 0.011 0.001 PHE C 88 TRP 0.039 0.002 TRP A 93 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00346 (10432) covalent geometry : angle 0.55234 (14154) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.21849 ( 8) hydrogen bonds : bond 0.17132 ( 477) hydrogen bonds : angle 7.41833 ( 1479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.398 Fit side-chains REVERT: A 93 TRP cc_start: 0.7617 (t60) cc_final: 0.6626 (t60) REVERT: C 93 TRP cc_start: 0.7517 (t60) cc_final: 0.6514 (t60) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.1186 time to fit residues: 22.2043 Evaluate side-chains 129 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.196959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130396 restraints weight = 9977.310| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.25 r_work: 0.3191 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10436 Z= 0.176 Angle : 0.543 8.890 14162 Z= 0.283 Chirality : 0.044 0.182 1628 Planarity : 0.004 0.049 1758 Dihedral : 4.747 56.947 1398 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 3.13 % Allowed : 20.21 % Favored : 76.65 % 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: 1.41 (0.24), residues: 1258 helix: 3.00 (0.24), residues: 422 sheet: -0.07 (0.33), residues: 254 loop : -0.11 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 199 TYR 0.017 0.001 TYR A 223 PHE 0.011 0.001 PHE A 118 TRP 0.016 0.001 TRP C 93 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00421 (10432) covalent geometry : angle 0.54264 (14154) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.19034 ( 8) hydrogen bonds : bond 0.03982 ( 477) hydrogen bonds : angle 4.95146 ( 1479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.404 Fit side-chains REVERT: A 93 TRP cc_start: 0.7760 (t60) cc_final: 0.6900 (t60) REVERT: A 172 MET cc_start: 0.7323 (tpt) cc_final: 0.7004 (tpt) REVERT: A 202 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7644 (ptm160) REVERT: C 93 TRP cc_start: 0.7725 (t60) cc_final: 0.6880 (t60) REVERT: C 149 MET cc_start: 0.7711 (mmm) cc_final: 0.7453 (mmm) REVERT: C 202 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: D 109 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7405 (p) outliers start: 35 outliers final: 13 residues processed: 162 average time/residue: 0.1022 time to fit residues: 23.2811 Evaluate side-chains 140 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN C 308 HIS D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.198395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133179 restraints weight = 10000.841| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.29 r_work: 0.3253 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10436 Z= 0.147 Angle : 0.509 8.612 14162 Z= 0.265 Chirality : 0.043 0.141 1628 Planarity : 0.004 0.049 1758 Dihedral : 4.634 59.334 1398 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.03 % Rotamer: Outliers : 3.76 % Allowed : 19.86 % Favored : 76.39 % 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: 1.48 (0.24), residues: 1258 helix: 2.98 (0.24), residues: 422 sheet: 0.10 (0.34), residues: 244 loop : -0.07 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 199 TYR 0.012 0.001 TYR A 223 PHE 0.010 0.001 PHE A 235 TRP 0.013 0.001 TRP A 85 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00349 (10432) covalent geometry : angle 0.50929 (14154) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.21160 ( 8) hydrogen bonds : bond 0.03608 ( 477) hydrogen bonds : angle 4.53160 ( 1479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.352 Fit side-chains REVERT: A 172 MET cc_start: 0.7209 (tpt) cc_final: 0.6840 (tpt) REVERT: A 202 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7548 (ptm160) REVERT: A 215 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8544 (m) REVERT: B 42 GLU cc_start: 0.7750 (pt0) cc_final: 0.7472 (pt0) REVERT: C 149 MET cc_start: 0.7724 (mmm) cc_final: 0.7501 (mmm) REVERT: C 172 MET cc_start: 0.7270 (tpt) cc_final: 0.7009 (tpt) REVERT: C 215 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8544 (m) REVERT: D 42 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6919 (mt-10) REVERT: D 62 MET cc_start: 0.7052 (tpt) cc_final: 0.6807 (tpt) REVERT: D 109 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7539 (p) outliers start: 42 outliers final: 18 residues processed: 174 average time/residue: 0.1000 time to fit residues: 24.5592 Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 111 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 308 HIS B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.198619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134613 restraints weight = 9993.427| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.31 r_work: 0.3275 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10436 Z= 0.123 Angle : 0.489 8.317 14162 Z= 0.254 Chirality : 0.042 0.142 1628 Planarity : 0.004 0.050 1758 Dihedral : 4.503 57.235 1398 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 4.20 % Allowed : 20.13 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1258 helix: 2.98 (0.24), residues: 422 sheet: 0.19 (0.34), residues: 244 loop : 0.01 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.022 0.001 TYR C 223 PHE 0.009 0.001 PHE A 235 TRP 0.023 0.001 TRP C 93 HIS 0.004 0.000 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00286 (10432) covalent geometry : angle 0.48896 (14154) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.20755 ( 8) hydrogen bonds : bond 0.03360 ( 477) hydrogen bonds : angle 4.30777 ( 1479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.384 Fit side-chains REVERT: A 93 TRP cc_start: 0.7696 (t60) cc_final: 0.6861 (t60) REVERT: A 202 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7520 (ptm160) REVERT: B 109 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7393 (p) REVERT: C 93 TRP cc_start: 0.7645 (t60) cc_final: 0.6808 (t60) REVERT: C 172 MET cc_start: 0.7455 (tpt) cc_final: 0.6995 (tpt) REVERT: C 202 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8113 (ptm160) REVERT: C 215 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8553 (m) REVERT: C 247 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (mp) REVERT: D 42 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6814 (mt-10) REVERT: D 62 MET cc_start: 0.7041 (tpt) cc_final: 0.6747 (tpt) REVERT: D 109 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7469 (p) REVERT: D 278 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8637 (tt0) outliers start: 47 outliers final: 22 residues processed: 178 average time/residue: 0.1075 time to fit residues: 26.7032 Evaluate side-chains 157 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 114 ASN B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133280 restraints weight = 10016.991| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.18 r_work: 0.3283 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10436 Z= 0.133 Angle : 0.495 8.198 14162 Z= 0.257 Chirality : 0.042 0.138 1628 Planarity : 0.004 0.050 1758 Dihedral : 4.513 56.099 1398 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.03 % Rotamer: Outliers : 4.38 % Allowed : 19.86 % Favored : 75.76 % 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: 1.57 (0.24), residues: 1258 helix: 2.98 (0.24), residues: 424 sheet: 0.17 (0.34), residues: 244 loop : 0.03 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.012 0.001 TYR A 223 PHE 0.010 0.001 PHE C 235 TRP 0.013 0.001 TRP C 85 HIS 0.002 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00317 (10432) covalent geometry : angle 0.49542 (14154) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.20502 ( 8) hydrogen bonds : bond 0.03312 ( 477) hydrogen bonds : angle 4.24074 ( 1479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.381 Fit side-chains REVERT: A 44 ASN cc_start: 0.8776 (t0) cc_final: 0.8532 (t0) REVERT: A 93 TRP cc_start: 0.7725 (t60) cc_final: 0.6888 (t60) REVERT: A 126 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 172 MET cc_start: 0.7310 (tpt) cc_final: 0.7029 (tpt) REVERT: A 202 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7639 (ptm160) REVERT: A 215 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8597 (m) REVERT: B 42 GLU cc_start: 0.7606 (pt0) cc_final: 0.7285 (pt0) REVERT: B 278 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 93 TRP cc_start: 0.7656 (t60) cc_final: 0.6848 (t60) REVERT: C 172 MET cc_start: 0.7543 (tpt) cc_final: 0.7001 (tpt) REVERT: C 202 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7819 (ptm160) REVERT: D 42 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6877 (mt-10) REVERT: D 109 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7501 (p) REVERT: D 278 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8420 (tt0) outliers start: 49 outliers final: 26 residues processed: 174 average time/residue: 0.1011 time to fit residues: 25.0691 Evaluate side-chains 159 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.196791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131691 restraints weight = 10074.430| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.16 r_work: 0.3254 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10436 Z= 0.164 Angle : 0.521 8.695 14162 Z= 0.269 Chirality : 0.043 0.138 1628 Planarity : 0.004 0.050 1758 Dihedral : 4.601 55.420 1398 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.47 % Rotamer: Outliers : 4.65 % Allowed : 19.77 % Favored : 75.58 % 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: 1.52 (0.24), residues: 1258 helix: 2.94 (0.23), residues: 424 sheet: 0.15 (0.33), residues: 254 loop : -0.01 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.019 0.001 TYR C 223 PHE 0.011 0.001 PHE C 235 TRP 0.018 0.001 TRP C 85 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00400 (10432) covalent geometry : angle 0.52092 (14154) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.33962 ( 8) hydrogen bonds : bond 0.03391 ( 477) hydrogen bonds : angle 4.27873 ( 1479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.383 Fit side-chains REVERT: A 126 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 172 MET cc_start: 0.7365 (tpt) cc_final: 0.6993 (tpt) REVERT: A 202 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7699 (ptm160) REVERT: A 215 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 42 GLU cc_start: 0.7610 (pt0) cc_final: 0.7244 (pt0) REVERT: B 266 LYS cc_start: 0.8010 (pttm) cc_final: 0.7677 (pttm) REVERT: B 278 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: C 149 MET cc_start: 0.7278 (mmm) cc_final: 0.6896 (mmm) REVERT: C 172 MET cc_start: 0.7600 (tpt) cc_final: 0.6949 (tpt) REVERT: C 197 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 202 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7748 (ptm160) REVERT: D 42 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 212 GLN cc_start: 0.8359 (tt0) cc_final: 0.7861 (tt0) REVERT: D 278 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8469 (tt0) outliers start: 52 outliers final: 33 residues processed: 181 average time/residue: 0.1120 time to fit residues: 27.9913 Evaluate side-chains 169 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.194849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131046 restraints weight = 10082.809| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.20 r_work: 0.3172 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10436 Z= 0.258 Angle : 0.600 9.252 14162 Z= 0.308 Chirality : 0.046 0.152 1628 Planarity : 0.005 0.050 1758 Dihedral : 4.869 52.831 1398 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.47 % Rotamer: Outliers : 4.47 % Allowed : 19.68 % Favored : 75.85 % 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: 1.28 (0.24), residues: 1258 helix: 2.86 (0.24), residues: 424 sheet: -0.07 (0.32), residues: 254 loop : -0.21 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 35 TYR 0.020 0.002 TYR A 223 PHE 0.015 0.002 PHE C 118 TRP 0.033 0.002 TRP A 93 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00640 (10432) covalent geometry : angle 0.60035 (14154) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.31231 ( 8) hydrogen bonds : bond 0.03736 ( 477) hydrogen bonds : angle 4.46905 ( 1479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.373 Fit side-chains REVERT: A 93 TRP cc_start: 0.7728 (t60) cc_final: 0.6801 (t60) REVERT: A 126 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7718 (tp) REVERT: A 172 MET cc_start: 0.7477 (tpt) cc_final: 0.7063 (tpt) REVERT: A 202 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7738 (ptm160) REVERT: A 215 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8464 (p) REVERT: A 311 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7018 (m-40) REVERT: B 278 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: C 93 TRP cc_start: 0.7735 (t60) cc_final: 0.6775 (t60) REVERT: C 172 MET cc_start: 0.7722 (tpt) cc_final: 0.7060 (tpt) REVERT: C 197 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 202 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7905 (ptm160) REVERT: C 320 TYR cc_start: 0.6787 (p90) cc_final: 0.6170 (p90) REVERT: D 42 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6974 (mt-10) REVERT: D 278 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8638 (tt0) outliers start: 50 outliers final: 34 residues processed: 175 average time/residue: 0.1063 time to fit residues: 25.9994 Evaluate side-chains 173 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 209 ASN B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.197592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.140554 restraints weight = 10015.234| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.95 r_work: 0.3243 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10436 Z= 0.141 Angle : 0.525 10.180 14162 Z= 0.270 Chirality : 0.042 0.142 1628 Planarity : 0.004 0.051 1758 Dihedral : 4.608 52.525 1398 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 3.85 % Allowed : 20.30 % Favored : 75.85 % 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: 1.41 (0.24), residues: 1258 helix: 2.89 (0.23), residues: 424 sheet: 0.04 (0.34), residues: 244 loop : -0.09 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 36 TYR 0.020 0.001 TYR C 223 PHE 0.012 0.001 PHE D 133 TRP 0.024 0.001 TRP C 93 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00338 (10432) covalent geometry : angle 0.52507 (14154) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.37576 ( 8) hydrogen bonds : bond 0.03349 ( 477) hydrogen bonds : angle 4.28874 ( 1479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.380 Fit side-chains REVERT: A 93 TRP cc_start: 0.7728 (t60) cc_final: 0.6861 (t60) REVERT: A 126 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 149 MET cc_start: 0.7579 (mmm) cc_final: 0.7315 (mmm) REVERT: A 202 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7565 (ptm160) REVERT: A 215 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8503 (m) REVERT: A 311 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.6882 (m-40) REVERT: B 278 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: C 93 TRP cc_start: 0.7685 (t60) cc_final: 0.6791 (t60) REVERT: C 172 MET cc_start: 0.7891 (tpt) cc_final: 0.7126 (tpt) REVERT: C 202 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7764 (ptm160) REVERT: C 247 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7910 (mp) REVERT: D 42 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6836 (mt-10) REVERT: D 278 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8396 (tt0) outliers start: 43 outliers final: 27 residues processed: 159 average time/residue: 0.1102 time to fit residues: 24.3964 Evaluate side-chains 158 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.199476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141635 restraints weight = 10068.026| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.90 r_work: 0.3275 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10436 Z= 0.122 Angle : 0.502 9.440 14162 Z= 0.259 Chirality : 0.042 0.144 1628 Planarity : 0.004 0.051 1758 Dihedral : 4.464 52.462 1398 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.40 % Allowed : 20.93 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1258 helix: 3.10 (0.23), residues: 416 sheet: 0.16 (0.34), residues: 244 loop : -0.01 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.010 0.001 TYR A 223 PHE 0.010 0.001 PHE C 235 TRP 0.022 0.001 TRP C 93 HIS 0.002 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00290 (10432) covalent geometry : angle 0.50218 (14154) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.34415 ( 8) hydrogen bonds : bond 0.03170 ( 477) hydrogen bonds : angle 4.15361 ( 1479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.389 Fit side-chains REVERT: A 126 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7588 (tp) REVERT: A 197 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7996 (tt) REVERT: A 202 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7595 (ptm160) REVERT: A 215 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8497 (m) REVERT: B 278 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: C 93 TRP cc_start: 0.7661 (t60) cc_final: 0.6797 (t60) REVERT: C 149 MET cc_start: 0.7600 (mmm) cc_final: 0.7274 (mmm) REVERT: C 172 MET cc_start: 0.7892 (tpt) cc_final: 0.7065 (tpt) REVERT: C 197 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (tp) REVERT: C 202 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7830 (ptm160) REVERT: C 247 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 320 TYR cc_start: 0.6824 (p90) cc_final: 0.6233 (p90) REVERT: D 42 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6838 (mt-10) REVERT: D 278 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8362 (tt0) outliers start: 38 outliers final: 22 residues processed: 159 average time/residue: 0.1006 time to fit residues: 22.5474 Evaluate side-chains 155 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN C 311 ASN D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.195965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138231 restraints weight = 9944.170| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.84 r_work: 0.3220 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10436 Z= 0.239 Angle : 0.582 8.882 14162 Z= 0.301 Chirality : 0.045 0.152 1628 Planarity : 0.005 0.050 1758 Dihedral : 4.759 50.606 1398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.07 % Rotamer: Outliers : 3.22 % Allowed : 21.38 % Favored : 75.40 % 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: 1.39 (0.24), residues: 1258 helix: 3.02 (0.23), residues: 416 sheet: -0.04 (0.32), residues: 254 loop : -0.15 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 36 TYR 0.017 0.001 TYR C 223 PHE 0.014 0.002 PHE A 235 TRP 0.040 0.002 TRP A 93 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00592 (10432) covalent geometry : angle 0.58259 (14154) SS BOND : bond 0.00049 ( 4) SS BOND : angle 0.31848 ( 8) hydrogen bonds : bond 0.03552 ( 477) hydrogen bonds : angle 4.38739 ( 1479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.374 Fit side-chains REVERT: A 93 TRP cc_start: 0.7800 (t60) cc_final: 0.6760 (t60) REVERT: A 197 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7928 (tt) REVERT: A 202 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.7791 (ptm160) REVERT: A 215 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8436 (p) REVERT: B 266 LYS cc_start: 0.7996 (pttm) cc_final: 0.7696 (pttm) REVERT: B 278 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: C 93 TRP cc_start: 0.7765 (t60) cc_final: 0.6862 (t60) REVERT: C 149 MET cc_start: 0.7785 (mmm) cc_final: 0.7430 (mmm) REVERT: C 172 MET cc_start: 0.7889 (tpt) cc_final: 0.7090 (tpt) REVERT: C 202 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7875 (ptm160) REVERT: C 320 TYR cc_start: 0.6919 (p90) cc_final: 0.6307 (p90) REVERT: D 42 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6944 (mt-10) REVERT: D 278 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8576 (tt0) outliers start: 36 outliers final: 27 residues processed: 158 average time/residue: 0.1148 time to fit residues: 25.0406 Evaluate side-chains 162 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 27 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 235 ASN C 114 ASN D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.198379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140828 restraints weight = 10065.443| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.91 r_work: 0.3264 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10436 Z= 0.139 Angle : 0.513 8.559 14162 Z= 0.267 Chirality : 0.042 0.140 1628 Planarity : 0.004 0.051 1758 Dihedral : 4.539 50.042 1398 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 2.95 % Allowed : 21.56 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1258 helix: 3.10 (0.23), residues: 416 sheet: 0.04 (0.34), residues: 244 loop : -0.03 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.009 0.001 TYR A 223 PHE 0.011 0.001 PHE D 133 TRP 0.037 0.002 TRP A 93 HIS 0.003 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00334 (10432) covalent geometry : angle 0.51296 (14154) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.34716 ( 8) hydrogen bonds : bond 0.03239 ( 477) hydrogen bonds : angle 4.22950 ( 1479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.95 seconds wall clock time: 56 minutes 35.00 seconds (3395.00 seconds total)