Starting phenix.real_space_refine on Fri Mar 6 15:21:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y59_10691/03_2026/6y59_10691.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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 S 45 5.16 5 C 10465 2.51 5 N 2575 2.21 5 O 2780 1.98 5 H 16045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31910 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.71, per 1000 atoms: 0.21 Number of scatterers: 31910 At special positions: 0 Unit cell: (95.68, 98.176, 156.416, 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 45 16.00 O 2780 8.00 N 2575 7.00 C 10465 6.00 H 16045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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: 2.87 Conformation dependent library (CDL) restraints added in 788.6 milliseconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3730 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 47.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.687A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 220 through 242 removed outlier: 4.429A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.565A pdb=" N LEU D 333 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 462 removed outlier: 5.595A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.687A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 462 removed outlier: 5.595A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 199 Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN B 147 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 42 removed outlier: 3.807A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN C 147 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 192 through 199 Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 192 through 199 Processing sheet with id=AC3, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN E 147 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 192 through 199 790 hydrogen bonds defined for protein. 2295 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: 7.27 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16035 1.03 - 1.23: 225 1.23 - 1.43: 6731 1.43 - 1.62: 9284 1.62 - 1.82: 70 Bond restraints: 32345 Sorted by residual: bond pdb=" N ILE C 100 " pdb=" CA ILE C 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.83e+00 bond pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.79e+00 bond pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.75e+00 bond pdb=" N ILE B 100 " pdb=" CA ILE B 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N ILE E 100 " pdb=" CA ILE E 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 32340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 50818 1.57 - 3.15: 6975 3.15 - 4.72: 617 4.72 - 6.29: 159 6.29 - 7.87: 31 Bond angle restraints: 58600 Sorted by residual: angle pdb=" CA PHE C 103 " pdb=" CB PHE C 103 " pdb=" CG PHE C 103 " ideal model delta sigma weight residual 113.80 119.94 -6.14 1.00e+00 1.00e+00 3.77e+01 angle pdb=" CA PHE D 103 " pdb=" CB PHE D 103 " pdb=" CG PHE D 103 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA PHE A 103 " pdb=" CB PHE A 103 " pdb=" CG PHE A 103 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA PHE E 103 " pdb=" CB PHE E 103 " pdb=" CG PHE E 103 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA PHE B 103 " pdb=" CB PHE B 103 " pdb=" CG PHE B 103 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 58595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13881 17.99 - 35.99: 984 35.99 - 53.98: 249 53.98 - 71.97: 41 71.97 - 89.97: 5 Dihedral angle restraints: 15160 sinusoidal: 8095 harmonic: 7065 Sorted by residual: dihedral pdb=" CA GLU E 250 " pdb=" C GLU E 250 " pdb=" N ARG E 251 " pdb=" CA ARG E 251 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU D 250 " pdb=" C GLU D 250 " pdb=" N ARG D 251 " pdb=" CA ARG D 251 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 250 " pdb=" C GLU A 250 " pdb=" N ARG A 251 " pdb=" CA ARG A 251 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1754 0.044 - 0.087: 560 0.087 - 0.131: 234 0.131 - 0.175: 37 0.175 - 0.218: 5 Chirality restraints: 2590 Sorted by residual: chirality pdb=" CA PHE B 103 " pdb=" N PHE B 103 " pdb=" C PHE B 103 " pdb=" CB PHE B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE E 103 " pdb=" N PHE E 103 " pdb=" C PHE E 103 " pdb=" CB PHE E 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE A 103 " pdb=" N PHE A 103 " pdb=" C PHE A 103 " pdb=" CB PHE A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2587 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE B 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 103 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 PHE B 103 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE B 103 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE B 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE B 103 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE E 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE E 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE E 103 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE E 103 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE E 103 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE E 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE E 103 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE D 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE D 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE D 103 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE D 103 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE D 103 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE D 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE D 103 " -0.017 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3297 2.25 - 2.84: 75188 2.84 - 3.43: 84987 3.43 - 4.01: 116717 4.01 - 4.60: 177116 Nonbonded interactions: 457305 Sorted by model distance: nonbonded pdb=" HH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 1.664 2.450 nonbonded pdb=" HH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 1.664 2.450 nonbonded pdb=" HH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 1.664 2.450 nonbonded pdb=" HH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 1.664 2.450 nonbonded pdb=" HH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 1.664 2.450 ... (remaining 457300 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.960 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: 0.180 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.540 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.008 0.057 16305 Z= 0.391 Angle : 0.945 7.868 22275 Z= 0.579 Chirality : 0.051 0.218 2590 Planarity : 0.005 0.037 2725 Dihedral : 12.318 54.978 5855 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -3.39 (0.18), residues: 1885 helix: -1.37 (0.15), residues: 780 sheet: -4.04 (0.16), residues: 445 loop : -1.59 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 219 TYR 0.011 0.002 TYR A 431 PHE 0.043 0.003 PHE E 103 TRP 0.024 0.002 TRP D 320 HIS 0.009 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00753 (16300) covalent geometry : angle 0.94483 (22265) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.67543 ( 10) hydrogen bonds : bond 0.16413 ( 790) hydrogen bonds : angle 7.90387 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4484 time to fit residues: 77.7255 Evaluate side-chains 84 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.046899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.036624 restraints weight = 311282.385| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.20 r_work: 0.2976 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16305 Z= 0.134 Angle : 0.569 5.054 22275 Z= 0.305 Chirality : 0.043 0.140 2590 Planarity : 0.004 0.034 2725 Dihedral : 4.800 20.906 2095 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.28 % Allowed : 4.96 % Favored : 94.76 % 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: -1.76 (0.20), residues: 1885 helix: 0.32 (0.17), residues: 810 sheet: -3.40 (0.18), residues: 445 loop : -1.11 (0.29), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 14 TYR 0.010 0.001 TYR E 116 PHE 0.013 0.001 PHE A 303 TRP 0.016 0.001 TRP D 320 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00291 (16300) covalent geometry : angle 0.56939 (22265) SS BOND : bond 0.00008 ( 5) SS BOND : angle 0.38674 ( 10) hydrogen bonds : bond 0.04406 ( 790) hydrogen bonds : angle 5.62457 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.4765 time to fit residues: 69.7871 Evaluate side-chains 80 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS E 119 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.044958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.034573 restraints weight = 316708.451| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.07 r_work: 0.2895 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16305 Z= 0.202 Angle : 0.575 5.177 22275 Z= 0.310 Chirality : 0.042 0.137 2590 Planarity : 0.004 0.038 2725 Dihedral : 4.433 18.385 2095 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.17 % Allowed : 5.63 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1885 helix: 0.98 (0.18), residues: 810 sheet: -2.83 (0.20), residues: 445 loop : -0.77 (0.29), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.008 0.001 TYR A 431 PHE 0.024 0.001 PHE B 303 TRP 0.015 0.001 TRP C 320 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00437 (16300) covalent geometry : angle 0.57474 (22265) SS BOND : bond 0.00085 ( 5) SS BOND : angle 0.32336 ( 10) hydrogen bonds : bond 0.04262 ( 790) hydrogen bonds : angle 5.24916 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 MET cc_start: 0.8734 (mmm) cc_final: 0.8470 (tmm) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 0.4382 time to fit residues: 55.4896 Evaluate side-chains 83 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.044136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.033819 restraints weight = 318576.606| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.94 r_work: 0.2870 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16305 Z= 0.186 Angle : 0.538 5.234 22275 Z= 0.289 Chirality : 0.041 0.136 2590 Planarity : 0.003 0.025 2725 Dihedral : 4.248 17.454 2095 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.95 % Allowed : 6.57 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1885 helix: 1.28 (0.18), residues: 810 sheet: -2.41 (0.22), residues: 445 loop : -0.61 (0.30), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.010 0.001 TYR A 116 PHE 0.025 0.001 PHE A 303 TRP 0.013 0.001 TRP B 320 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00399 (16300) covalent geometry : angle 0.53772 (22265) SS BOND : bond 0.00056 ( 5) SS BOND : angle 0.28534 ( 10) hydrogen bonds : bond 0.03861 ( 790) hydrogen bonds : angle 4.95928 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 MET cc_start: 0.8684 (mmm) cc_final: 0.8430 (tmm) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.5145 time to fit residues: 57.1075 Evaluate side-chains 82 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.043151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032869 restraints weight = 321536.219| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.85 r_work: 0.2836 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16305 Z= 0.237 Angle : 0.569 5.381 22275 Z= 0.310 Chirality : 0.041 0.138 2590 Planarity : 0.003 0.024 2725 Dihedral : 4.308 19.801 2095 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.39 % Allowed : 6.63 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1885 helix: 1.26 (0.17), residues: 810 sheet: -2.46 (0.22), residues: 475 loop : -0.49 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.009 0.001 TYR E 431 PHE 0.020 0.001 PHE A 438 TRP 0.012 0.001 TRP D 320 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00512 (16300) covalent geometry : angle 0.56926 (22265) SS BOND : bond 0.00086 ( 5) SS BOND : angle 0.34002 ( 10) hydrogen bonds : bond 0.04082 ( 790) hydrogen bonds : angle 4.94988 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.8601 (t70) REVERT: C 210 MET cc_start: 0.8749 (mmm) cc_final: 0.8459 (tmm) outliers start: 25 outliers final: 23 residues processed: 90 average time/residue: 0.4808 time to fit residues: 58.0422 Evaluate side-chains 87 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 451 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.043386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033113 restraints weight = 317051.376| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.79 r_work: 0.2846 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16305 Z= 0.167 Angle : 0.510 5.674 22275 Z= 0.275 Chirality : 0.041 0.138 2590 Planarity : 0.003 0.025 2725 Dihedral : 4.132 17.320 2095 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.39 % Allowed : 7.41 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1885 helix: 1.55 (0.17), residues: 810 sheet: -2.28 (0.23), residues: 475 loop : -0.36 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.008 0.001 TYR E 431 PHE 0.021 0.001 PHE A 438 TRP 0.013 0.001 TRP A 320 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00364 (16300) covalent geometry : angle 0.51047 (22265) SS BOND : bond 0.00060 ( 5) SS BOND : angle 0.18923 ( 10) hydrogen bonds : bond 0.03689 ( 790) hydrogen bonds : angle 4.71496 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 MET cc_start: 0.8753 (mmm) cc_final: 0.8441 (tmm) REVERT: C 235 MET cc_start: 0.9367 (mtt) cc_final: 0.8884 (mmm) outliers start: 25 outliers final: 23 residues processed: 87 average time/residue: 0.4510 time to fit residues: 52.9195 Evaluate side-chains 84 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 451 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.044019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033686 restraints weight = 316361.766| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.83 r_work: 0.2863 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16305 Z= 0.114 Angle : 0.477 5.466 22275 Z= 0.253 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.025 2725 Dihedral : 3.906 16.270 2095 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.06 % Allowed : 8.52 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1885 helix: 1.88 (0.18), residues: 810 sheet: -2.03 (0.23), residues: 475 loop : -0.17 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 428 TYR 0.007 0.001 TYR E 431 PHE 0.023 0.001 PHE A 438 TRP 0.013 0.001 TRP A 320 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00256 (16300) covalent geometry : angle 0.47747 (22265) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.13167 ( 10) hydrogen bonds : bond 0.03275 ( 790) hydrogen bonds : angle 4.44221 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9431 (mtt) cc_final: 0.8907 (mmm) REVERT: C 210 MET cc_start: 0.8757 (mmm) cc_final: 0.8397 (tmm) REVERT: C 428 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8216 (ppt90) REVERT: E 210 MET cc_start: 0.8522 (ttm) cc_final: 0.8163 (ttm) outliers start: 19 outliers final: 17 residues processed: 82 average time/residue: 0.4731 time to fit residues: 51.7643 Evaluate side-chains 83 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 451 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 144 optimal weight: 0.0270 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.043792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033514 restraints weight = 316408.347| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.74 r_work: 0.2857 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16305 Z= 0.137 Angle : 0.479 5.629 22275 Z= 0.255 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.025 2725 Dihedral : 3.849 15.656 2095 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.06 % Allowed : 8.69 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1885 helix: 1.91 (0.18), residues: 825 sheet: -1.96 (0.23), residues: 475 loop : -0.20 (0.31), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 328 TYR 0.006 0.001 TYR A 441 PHE 0.028 0.001 PHE A 438 TRP 0.012 0.001 TRP A 320 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00304 (16300) covalent geometry : angle 0.47923 (22265) SS BOND : bond 0.00072 ( 5) SS BOND : angle 0.15739 ( 10) hydrogen bonds : bond 0.03250 ( 790) hydrogen bonds : angle 4.40165 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9428 (mtt) cc_final: 0.8860 (mmm) REVERT: C 210 MET cc_start: 0.8741 (mmm) cc_final: 0.8411 (tmm) REVERT: E 210 MET cc_start: 0.8471 (ttm) cc_final: 0.7607 (mtp) outliers start: 19 outliers final: 18 residues processed: 80 average time/residue: 0.4832 time to fit residues: 51.4340 Evaluate side-chains 83 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.043233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033167 restraints weight = 318527.739| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.61 r_work: 0.2847 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16305 Z= 0.188 Angle : 0.512 5.554 22275 Z= 0.276 Chirality : 0.041 0.138 2590 Planarity : 0.003 0.025 2725 Dihedral : 3.949 16.708 2095 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 8.75 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1885 helix: 1.85 (0.17), residues: 825 sheet: -2.06 (0.22), residues: 475 loop : -0.26 (0.31), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 428 TYR 0.007 0.001 TYR B 448 PHE 0.019 0.001 PHE A 438 TRP 0.011 0.001 TRP C 426 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00412 (16300) covalent geometry : angle 0.51188 (22265) SS BOND : bond 0.00094 ( 5) SS BOND : angle 0.18416 ( 10) hydrogen bonds : bond 0.03505 ( 790) hydrogen bonds : angle 4.48826 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 MET cc_start: 0.8726 (mmm) cc_final: 0.8395 (tmm) REVERT: E 210 MET cc_start: 0.8431 (ttm) cc_final: 0.7550 (mtp) outliers start: 21 outliers final: 20 residues processed: 81 average time/residue: 0.4813 time to fit residues: 52.1864 Evaluate side-chains 83 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 126 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.044161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.033901 restraints weight = 312629.520| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.72 r_work: 0.2873 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16305 Z= 0.101 Angle : 0.467 6.101 22275 Z= 0.246 Chirality : 0.041 0.136 2590 Planarity : 0.003 0.026 2725 Dihedral : 3.772 15.170 2095 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.06 % Allowed : 8.86 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1885 helix: 2.10 (0.18), residues: 825 sheet: -1.97 (0.22), residues: 475 loop : -0.20 (0.30), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 428 TYR 0.008 0.001 TYR A 441 PHE 0.028 0.001 PHE A 438 TRP 0.012 0.001 TRP E 320 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00231 (16300) covalent geometry : angle 0.46679 (22265) SS BOND : bond 0.00063 ( 5) SS BOND : angle 0.11613 ( 10) hydrogen bonds : bond 0.03097 ( 790) hydrogen bonds : angle 4.25690 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 MET cc_start: 0.8715 (mmm) cc_final: 0.8342 (tmm) REVERT: E 210 MET cc_start: 0.8454 (ttm) cc_final: 0.7622 (mtp) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.4731 time to fit residues: 50.6506 Evaluate side-chains 79 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 57 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034404 restraints weight = 311294.842| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.73 r_work: 0.2891 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 16305 Z= 0.088 Angle : 0.469 10.091 22275 Z= 0.243 Chirality : 0.042 0.192 2590 Planarity : 0.003 0.027 2725 Dihedral : 3.648 14.823 2095 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.84 % Allowed : 9.30 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1885 helix: 2.22 (0.18), residues: 825 sheet: -1.83 (0.23), residues: 475 loop : -0.16 (0.30), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 428 TYR 0.008 0.001 TYR A 441 PHE 0.019 0.001 PHE A 438 TRP 0.016 0.001 TRP C 426 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00211 (16300) covalent geometry : angle 0.46882 (22265) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.11952 ( 10) hydrogen bonds : bond 0.02818 ( 790) hydrogen bonds : angle 4.11969 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6831.11 seconds wall clock time: 116 minutes 42.24 seconds (7002.24 seconds total)