Starting phenix.real_space_refine on Fri Mar 6 03:56:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m79_30128/03_2026/6m79_30128.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15296 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 64 5.16 5 C 9858 2.51 5 N 2610 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 15324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3750 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3828 Chain: "B" Number of atoms: 3760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 bond proxies already assigned to first conformer: 3854 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'AMP%rna3p': 1, 'FAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'AMP%rna3p': 1, 'FAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Restraints were copied for chains: C, D Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN A 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 356 " occ=0.50 residue: pdb=" N AASP A 473 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP A 473 " occ=0.51 residue: pdb=" N AASN B 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 356 " occ=0.50 residue: pdb=" N AASN C 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 356 " occ=0.50 residue: pdb=" N AASP C 473 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP C 473 " occ=0.51 residue: pdb=" N AASN D 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 356 " occ=0.50 Time building chain proxies: 5.93, per 1000 atoms: 0.39 Number of scatterers: 15324 At special positions: 0 Unit cell: (136.53, 109.89, 119.88, 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 64 16.00 P 12 15.00 O 2780 8.00 N 2610 7.00 C 9858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 62.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.041A pdb=" N GLU A 43 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 49 through 71 removed outlier: 3.625A pdb=" N TRP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.652A pdb=" N ALA A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.653A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.672A pdb=" N PHE A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 275 Processing helix chain 'A' and resid 277 through 304 removed outlier: 4.019A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.762A pdb=" N PHE A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.598A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.968A pdb=" N GLY A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.584A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.041A pdb=" N GLU B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 49 through 71 removed outlier: 3.625A pdb=" N TRP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.652A pdb=" N ALA B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.653A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.673A pdb=" N PHE B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 275 Processing helix chain 'B' and resid 277 through 304 removed outlier: 4.019A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.762A pdb=" N PHE B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.597A pdb=" N ALA B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 369 Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.967A pdb=" N GLY B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 402 Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.585A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 452 through 459 Processing helix chain 'B' and resid 473 through 487 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.041A pdb=" N GLU C 43 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 49 through 71 removed outlier: 3.625A pdb=" N TRP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 removed outlier: 3.652A pdb=" N ALA C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.654A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.673A pdb=" N PHE C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 275 Processing helix chain 'C' and resid 277 through 304 removed outlier: 4.019A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.763A pdb=" N PHE C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.597A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 369 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.968A pdb=" N GLY C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 402 Processing helix chain 'C' and resid 415 through 424 Processing helix chain 'C' and resid 427 through 434 removed outlier: 3.584A pdb=" N TRP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 438 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 473 through 484 Processing helix chain 'D' and resid 20 through 30 Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.042A pdb=" N GLU D 43 " --> pdb=" O CYS D 39 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 44' Processing helix chain 'D' and resid 49 through 71 removed outlier: 3.625A pdb=" N TRP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 removed outlier: 3.652A pdb=" N ALA D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.653A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.672A pdb=" N PHE D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 275 Processing helix chain 'D' and resid 277 through 304 removed outlier: 4.018A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.762A pdb=" N PHE D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.597A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.968A pdb=" N GLY D 377 " --> pdb=" O PRO D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 402 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.585A pdb=" N TRP D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 438 Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 473 through 487 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.532A pdb=" N VAL A 9 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE A 37 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS A 6 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL A 99 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 8 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN A 101 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP A 10 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.532A pdb=" N VAL B 9 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 37 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 6 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL B 99 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 8 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN B 101 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP B 10 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.532A pdb=" N VAL C 9 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE C 37 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 6 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL C 99 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 8 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN C 101 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP C 10 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.532A pdb=" N VAL D 9 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE D 37 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS D 6 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL D 99 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 8 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN D 101 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP D 10 " --> pdb=" O ASN D 101 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 2244 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: 2.24 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4817 1.34 - 1.46: 2806 1.46 - 1.57: 8077 1.57 - 1.69: 8 1.69 - 1.81: 96 Bond restraints: 15804 Sorted by residual: bond pdb=" O3P FAD D 702 " pdb=" P FAD D 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O3P FAD C 702 " pdb=" P FAD C 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3P FAD B 702 " pdb=" P FAD B 702 " ideal model delta sigma weight residual 1.660 1.565 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O5B FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sigma weight residual 1.634 1.541 0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 15799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 20984 1.99 - 3.98: 470 3.98 - 5.97: 80 5.97 - 7.96: 8 7.96 - 9.95: 12 Bond angle restraints: 21554 Sorted by residual: angle pdb=" C1' AMP B 701 " pdb=" C2' AMP B 701 " pdb=" C3' AMP B 701 " ideal model delta sigma weight residual 111.00 101.05 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C1' AMP D 701 " pdb=" C2' AMP D 701 " pdb=" C3' AMP D 701 " ideal model delta sigma weight residual 111.00 101.09 9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C1' AMP C 701 " pdb=" C2' AMP C 701 " pdb=" C3' AMP C 701 " ideal model delta sigma weight residual 111.00 101.10 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C1' AMP A 701 " pdb=" C2' AMP A 701 " pdb=" C3' AMP A 701 " ideal model delta sigma weight residual 111.00 101.10 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C ASN A 303 " pdb=" N PHE A 304 " pdb=" CA PHE A 304 " ideal model delta sigma weight residual 123.16 119.78 3.38 1.23e+00 6.61e-01 7.53e+00 ... (remaining 21549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 8578 20.26 - 40.51: 538 40.51 - 60.76: 136 60.76 - 81.02: 56 81.02 - 101.27: 18 Dihedral angle restraints: 9326 sinusoidal: 3946 harmonic: 5380 Sorted by residual: dihedral pdb=" C5' AMP B 701 " pdb=" O5' AMP B 701 " pdb=" P AMP B 701 " pdb=" O3P AMP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 41.28 -101.27 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C5' AMP D 701 " pdb=" O5' AMP D 701 " pdb=" P AMP D 701 " pdb=" O3P AMP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 41.26 -101.26 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" CB GLU C 282 " pdb=" CG GLU C 282 " pdb=" CD GLU C 282 " pdb=" OE1 GLU C 282 " ideal model delta sinusoidal sigma weight residual 0.00 88.08 -88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 9323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1520 0.046 - 0.092: 614 0.092 - 0.138: 116 0.138 - 0.184: 12 0.184 - 0.230: 4 Chirality restraints: 2266 Sorted by residual: chirality pdb=" C2' AMP A 701 " pdb=" C1' AMP A 701 " pdb=" C3' AMP A 701 " pdb=" O2' AMP A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2' AMP D 701 " pdb=" C1' AMP D 701 " pdb=" C3' AMP D 701 " pdb=" O2' AMP D 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C2' AMP B 701 " pdb=" C1' AMP B 701 " pdb=" C3' AMP B 701 " pdb=" O2' AMP B 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2263 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 338 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 339 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 339 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 338 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO C 339 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " 0.022 5.00e-02 4.00e+02 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 178 2.63 - 3.20: 13204 3.20 - 3.77: 21751 3.77 - 4.33: 29308 4.33 - 4.90: 50774 Nonbonded interactions: 115215 Sorted by model distance: nonbonded pdb=" O TYR D 232 " pdb=" OG SER D 236 " model vdw 2.067 3.040 nonbonded pdb=" O TYR A 232 " pdb=" OG SER A 236 " model vdw 2.067 3.040 nonbonded pdb=" O TYR C 232 " pdb=" OG SER C 236 " model vdw 2.067 3.040 nonbonded pdb=" O TYR B 232 " pdb=" OG SER B 236 " model vdw 2.067 3.040 nonbonded pdb=" O ARG D 359 " pdb=" OG SER D 363 " model vdw 2.119 3.040 ... (remaining 115210 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 0.115 15808 Z= 0.397 Angle : 0.786 9.947 21554 Z= 0.419 Chirality : 0.049 0.230 2266 Planarity : 0.004 0.040 2672 Dihedral : 16.076 101.273 5850 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.99 % Allowed : 7.47 % Favored : 88.54 % 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: -0.35 (0.19), residues: 1832 helix: 0.81 (0.16), residues: 1024 sheet: -0.02 (0.46), residues: 132 loop : -1.91 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 91 TYR 0.018 0.002 TYR B 299 PHE 0.013 0.002 PHE D 100 TRP 0.014 0.002 TRP B 214 HIS 0.007 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00797 (15804) covalent geometry : angle 0.78556 (21554) hydrogen bonds : bond 0.12206 ( 768) hydrogen bonds : angle 5.32576 ( 2244) Misc. bond : bond 0.11495 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7925 (mt) cc_final: 0.7661 (mt) REVERT: A 345 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmm) REVERT: A 474 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5329 (tt) REVERT: B 28 HIS cc_start: 0.7583 (t-90) cc_final: 0.7272 (t-90) REVERT: B 345 MET cc_start: 0.8587 (mmm) cc_final: 0.8178 (mmp) REVERT: B 422 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: B 479 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5023 (tp30) REVERT: C 86 ILE cc_start: 0.7943 (mt) cc_final: 0.7694 (mt) REVERT: C 345 MET cc_start: 0.8453 (mmm) cc_final: 0.8136 (mmm) REVERT: C 474 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5322 (tt) REVERT: D 28 HIS cc_start: 0.7571 (t-90) cc_final: 0.7252 (t-90) REVERT: D 345 MET cc_start: 0.8589 (mmm) cc_final: 0.8191 (mmp) REVERT: D 422 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: D 479 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5017 (tp30) outliers start: 60 outliers final: 28 residues processed: 275 average time/residue: 0.1314 time to fit residues: 52.4965 Evaluate side-chains 191 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121359 restraints weight = 69401.265| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.32 r_work: 0.3130 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15808 Z= 0.128 Angle : 0.619 7.691 21554 Z= 0.308 Chirality : 0.043 0.140 2266 Planarity : 0.004 0.033 2672 Dihedral : 10.451 77.917 2284 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.68 % Allowed : 10.71 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.19), residues: 1832 helix: 1.39 (0.16), residues: 1040 sheet: 0.19 (0.47), residues: 132 loop : -1.75 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.010 0.001 TYR C 47 PHE 0.010 0.001 PHE C 46 TRP 0.014 0.001 TRP B 214 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00267 (15804) covalent geometry : angle 0.61882 (21554) hydrogen bonds : bond 0.05643 ( 768) hydrogen bonds : angle 4.44259 ( 2244) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.519 Fit side-chains REVERT: A 266 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7407 (tpt90) REVERT: A 345 MET cc_start: 0.8596 (mmm) cc_final: 0.8343 (mmm) REVERT: B 266 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7640 (tpt170) REVERT: B 345 MET cc_start: 0.8689 (mmm) cc_final: 0.8352 (mmp) REVERT: C 266 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7396 (tpt90) REVERT: C 345 MET cc_start: 0.8612 (mmm) cc_final: 0.8361 (mmm) REVERT: D 266 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7658 (tpt170) REVERT: D 345 MET cc_start: 0.8692 (mmm) cc_final: 0.8362 (mmp) outliers start: 23 outliers final: 12 residues processed: 194 average time/residue: 0.1317 time to fit residues: 37.2577 Evaluate side-chains 168 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 266 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114284 restraints weight = 56533.800| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.89 r_work: 0.3063 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 15808 Z= 0.330 Angle : 0.809 9.327 21554 Z= 0.405 Chirality : 0.053 0.186 2266 Planarity : 0.006 0.044 2672 Dihedral : 10.152 68.375 2240 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.18 % Allowed : 12.14 % Favored : 85.68 % 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: -0.28 (0.19), residues: 1832 helix: 0.89 (0.16), residues: 1020 sheet: 0.18 (0.46), residues: 132 loop : -1.96 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.018 0.002 TYR A 299 PHE 0.022 0.003 PHE D 100 TRP 0.017 0.002 TRP A 214 HIS 0.011 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00794 (15804) covalent geometry : angle 0.80926 (21554) hydrogen bonds : bond 0.09244 ( 768) hydrogen bonds : angle 4.85521 ( 2244) Misc. bond : bond 0.00128 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 266 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7537 (tpt90) REVERT: A 301 CYS cc_start: 0.7982 (t) cc_final: 0.7188 (m) REVERT: A 447 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.7892 (p90) REVERT: B 282 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7845 (mt-10) REVERT: C 119 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7980 (tp) REVERT: C 266 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7555 (tpt90) REVERT: C 301 CYS cc_start: 0.7979 (t) cc_final: 0.7193 (m) REVERT: C 447 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.7894 (p90) REVERT: D 282 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7797 (mt-10) outliers start: 31 outliers final: 16 residues processed: 184 average time/residue: 0.1304 time to fit residues: 34.8006 Evaluate side-chains 175 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121422 restraints weight = 62803.791| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.11 r_work: 0.3158 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15808 Z= 0.121 Angle : 0.583 6.579 21554 Z= 0.288 Chirality : 0.042 0.141 2266 Planarity : 0.004 0.033 2672 Dihedral : 8.730 71.634 2236 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.68 % Allowed : 13.70 % Favored : 84.62 % 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: 0.38 (0.19), residues: 1832 helix: 1.40 (0.16), residues: 1038 sheet: 0.28 (0.47), residues: 132 loop : -1.65 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 12 TYR 0.008 0.001 TYR C 47 PHE 0.008 0.001 PHE B 100 TRP 0.015 0.001 TRP A 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00254 (15804) covalent geometry : angle 0.58259 (21554) hydrogen bonds : bond 0.05288 ( 768) hydrogen bonds : angle 4.39449 ( 2244) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.639 Fit side-chains REVERT: A 301 CYS cc_start: 0.7682 (t) cc_final: 0.7078 (m) REVERT: A 447 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8164 (p90) REVERT: C 266 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7383 (tpt170) REVERT: C 301 CYS cc_start: 0.7691 (t) cc_final: 0.7087 (m) REVERT: C 447 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8164 (p90) outliers start: 23 outliers final: 12 residues processed: 187 average time/residue: 0.1259 time to fit residues: 34.5225 Evaluate side-chains 179 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 110 optimal weight: 0.0270 chunk 95 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119724 restraints weight = 84143.706| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.39 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15808 Z= 0.137 Angle : 0.593 6.857 21554 Z= 0.292 Chirality : 0.042 0.136 2266 Planarity : 0.004 0.032 2672 Dihedral : 8.555 67.548 2236 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.12 % Allowed : 14.26 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1832 helix: 1.53 (0.16), residues: 1038 sheet: 0.24 (0.47), residues: 132 loop : -1.56 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 266 TYR 0.022 0.001 TYR B 299 PHE 0.010 0.001 PHE B 100 TRP 0.011 0.001 TRP C 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00305 (15804) covalent geometry : angle 0.59309 (21554) hydrogen bonds : bond 0.05696 ( 768) hydrogen bonds : angle 4.35492 ( 2244) Misc. bond : bond 0.00048 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.642 Fit side-chains REVERT: A 191 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7242 (tt0) REVERT: A 301 CYS cc_start: 0.7641 (t) cc_final: 0.7146 (m) REVERT: C 301 CYS cc_start: 0.7584 (t) cc_final: 0.7057 (m) outliers start: 14 outliers final: 13 residues processed: 176 average time/residue: 0.1206 time to fit residues: 31.5197 Evaluate side-chains 168 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119613 restraints weight = 77313.281| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 4.41 r_work: 0.3110 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.148 Angle : 0.601 6.721 21554 Z= 0.297 Chirality : 0.043 0.137 2266 Planarity : 0.004 0.033 2672 Dihedral : 8.529 67.041 2234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 13.95 % Favored : 84.68 % 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: 0.57 (0.20), residues: 1832 helix: 1.54 (0.16), residues: 1038 sheet: 0.19 (0.46), residues: 132 loop : -1.50 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 266 TYR 0.021 0.001 TYR D 299 PHE 0.011 0.002 PHE D 100 TRP 0.013 0.001 TRP A 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00337 (15804) covalent geometry : angle 0.60129 (21554) hydrogen bonds : bond 0.05893 ( 768) hydrogen bonds : angle 4.36587 ( 2244) Misc. bond : bond 0.00052 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.587 Fit side-chains REVERT: A 191 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7684 (tt0) REVERT: A 447 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8349 (p90) REVERT: B 326 ASP cc_start: 0.7584 (m-30) cc_final: 0.6899 (p0) REVERT: C 191 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7738 (tt0) REVERT: C 447 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (p90) REVERT: D 326 ASP cc_start: 0.7570 (m-30) cc_final: 0.6890 (p0) outliers start: 18 outliers final: 16 residues processed: 170 average time/residue: 0.1134 time to fit residues: 29.2811 Evaluate side-chains 164 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 135 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.153343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122347 restraints weight = 73536.796| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.47 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15808 Z= 0.109 Angle : 0.550 5.891 21554 Z= 0.269 Chirality : 0.041 0.135 2266 Planarity : 0.003 0.031 2672 Dihedral : 8.175 68.306 2234 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 14.38 % Favored : 84.37 % 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: 0.87 (0.20), residues: 1832 helix: 1.79 (0.16), residues: 1036 sheet: 0.13 (0.46), residues: 134 loop : -1.33 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 12 TYR 0.020 0.001 TYR D 299 PHE 0.008 0.001 PHE A 46 TRP 0.013 0.001 TRP B 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00236 (15804) covalent geometry : angle 0.55027 (21554) hydrogen bonds : bond 0.04596 ( 768) hydrogen bonds : angle 4.22677 ( 2244) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.612 Fit side-chains REVERT: A 191 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7118 (tt0) REVERT: A 447 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8068 (p90) REVERT: B 172 TRP cc_start: 0.6073 (t60) cc_final: 0.5793 (t-100) REVERT: B 326 ASP cc_start: 0.7340 (m-30) cc_final: 0.6961 (p0) REVERT: C 191 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7220 (tt0) REVERT: C 447 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8065 (p90) REVERT: D 326 ASP cc_start: 0.7365 (m-30) cc_final: 0.6979 (p0) outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 0.1229 time to fit residues: 32.5476 Evaluate side-chains 165 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 9 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119987 restraints weight = 70721.584| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.36 r_work: 0.3151 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15808 Z= 0.185 Angle : 0.643 7.527 21554 Z= 0.317 Chirality : 0.045 0.143 2266 Planarity : 0.004 0.032 2672 Dihedral : 8.728 64.068 2234 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 14.01 % Favored : 84.43 % 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: 0.53 (0.20), residues: 1832 helix: 1.50 (0.16), residues: 1042 sheet: 0.18 (0.46), residues: 132 loop : -1.51 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 12 TYR 0.020 0.002 TYR B 299 PHE 0.013 0.002 PHE D 100 TRP 0.013 0.001 TRP A 214 HIS 0.006 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00431 (15804) covalent geometry : angle 0.64294 (21554) hydrogen bonds : bond 0.06639 ( 768) hydrogen bonds : angle 4.39506 ( 2244) Misc. bond : bond 0.00072 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.441 Fit side-chains REVERT: A 191 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7808 (tt0) REVERT: A 345 MET cc_start: 0.8294 (mmm) cc_final: 0.7859 (mmm) REVERT: A 447 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8257 (p90) REVERT: B 172 TRP cc_start: 0.6279 (t60) cc_final: 0.5975 (t-100) REVERT: B 326 ASP cc_start: 0.7558 (m-30) cc_final: 0.6893 (p0) REVERT: C 73 ASP cc_start: 0.8132 (t0) cc_final: 0.7929 (m-30) REVERT: C 191 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7855 (tt0) REVERT: C 345 MET cc_start: 0.8314 (mmm) cc_final: 0.7916 (mmm) REVERT: C 447 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8247 (p90) REVERT: D 326 ASP cc_start: 0.7553 (m-30) cc_final: 0.6875 (p0) outliers start: 21 outliers final: 19 residues processed: 173 average time/residue: 0.1144 time to fit residues: 30.2336 Evaluate side-chains 171 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 178 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119891 restraints weight = 78013.340| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.53 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15808 Z= 0.150 Angle : 0.603 7.319 21554 Z= 0.297 Chirality : 0.043 0.136 2266 Planarity : 0.004 0.031 2672 Dihedral : 8.548 66.345 2234 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.62 % Allowed : 13.89 % Favored : 84.50 % 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: 0.60 (0.20), residues: 1832 helix: 1.55 (0.16), residues: 1040 sheet: 0.12 (0.45), residues: 132 loop : -1.44 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.024 0.001 TYR B 299 PHE 0.011 0.001 PHE B 100 TRP 0.016 0.001 TRP B 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00344 (15804) covalent geometry : angle 0.60280 (21554) hydrogen bonds : bond 0.05905 ( 768) hydrogen bonds : angle 4.33859 ( 2244) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.579 Fit side-chains REVERT: A 191 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7250 (tt0) REVERT: A 447 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8069 (p90) REVERT: B 172 TRP cc_start: 0.6107 (t60) cc_final: 0.5836 (t-100) REVERT: B 326 ASP cc_start: 0.7404 (m-30) cc_final: 0.6929 (p0) REVERT: C 73 ASP cc_start: 0.7867 (t0) cc_final: 0.7645 (m-30) REVERT: C 191 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7313 (tt0) REVERT: C 447 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8059 (p90) REVERT: D 326 ASP cc_start: 0.7433 (m-30) cc_final: 0.6941 (p0) outliers start: 22 outliers final: 17 residues processed: 170 average time/residue: 0.1140 time to fit residues: 29.4457 Evaluate side-chains 169 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 145 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.155840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125356 restraints weight = 76118.982| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.30 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15808 Z= 0.100 Angle : 0.539 6.988 21554 Z= 0.263 Chirality : 0.040 0.135 2266 Planarity : 0.003 0.031 2672 Dihedral : 7.993 68.337 2234 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.25 % Allowed : 14.32 % Favored : 84.43 % 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: 1.06 (0.20), residues: 1832 helix: 1.89 (0.16), residues: 1042 sheet: 0.15 (0.45), residues: 134 loop : -1.16 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.023 0.001 TYR D 299 PHE 0.010 0.001 PHE A 46 TRP 0.013 0.001 TRP B 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00210 (15804) covalent geometry : angle 0.53865 (21554) hydrogen bonds : bond 0.03984 ( 768) hydrogen bonds : angle 4.16452 ( 2244) Misc. bond : bond 0.00019 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.535 Fit side-chains REVERT: A 191 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7201 (tt0) REVERT: C 191 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7316 (tt0) REVERT: D 326 ASP cc_start: 0.7417 (m-30) cc_final: 0.6996 (p0) outliers start: 16 outliers final: 10 residues processed: 173 average time/residue: 0.1125 time to fit residues: 29.9141 Evaluate side-chains 159 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.150854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120029 restraints weight = 75368.930| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.37 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15808 Z= 0.186 Angle : 0.638 7.564 21554 Z= 0.314 Chirality : 0.045 0.142 2266 Planarity : 0.004 0.031 2672 Dihedral : 8.600 63.741 2234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.00 % Allowed : 14.63 % Favored : 84.37 % 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: 0.77 (0.20), residues: 1832 helix: 1.64 (0.16), residues: 1042 sheet: 0.18 (0.46), residues: 134 loop : -1.30 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 12 TYR 0.023 0.002 TYR D 299 PHE 0.012 0.002 PHE D 100 TRP 0.012 0.001 TRP A 214 HIS 0.008 0.002 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00435 (15804) covalent geometry : angle 0.63808 (21554) hydrogen bonds : bond 0.06376 ( 768) hydrogen bonds : angle 4.37077 ( 2244) Misc. bond : bond 0.00077 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.71 seconds wall clock time: 53 minutes 50.75 seconds (3230.75 seconds total)