Starting phenix.real_space_refine on Mon Sep 14 03:57:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m79_30128/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.map" model { file = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m79_30128/09_2026/6m79_30128.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'FAD': 1} Classifications: {'RNAv2': 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: {'FAD': 1} Classifications: {'RNAv2': 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: 6.52, per 1000 atoms: 0.43 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: 1.42 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: 0.42 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: 2.27 Time building geometry restraints manager: 1.83 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: 8522 20.26 - 40.51: 494 40.51 - 60.76: 96 60.76 - 81.02: 24 81.02 - 101.27: 18 Dihedral angle restraints: 9154 sinusoidal: 3774 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 9151 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: 0.03 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: 1.110 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.510 Find NCS groups from input model: 0.130 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 14.673 101.273 5678 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/Z covalent geometry : bond 0.00797 / 0.35 (15804) covalent geometry : angle 0.78556 / 0.42 (21554) hydrogen bonds : bond 0.12206 / 8.40 ( 768) hydrogen bonds : angle 5.32576 / 3.78 ( 2244) Misc. bond : bond 0.11495 / 5.76 ( 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 : 0.598 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: 0.1332 time to fit residues: 53.2755 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 : 0.596 ------------------------------------------------------------------------------- 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... 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 = 0.3774 r_free = 0.3774 target = 0.152848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121847 restraints weight = 69462.451| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.40 r_work: 0.3164 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15808 Z= 0.126 Angle : 0.609 7.992 21554 Z= 0.306 Chirality : 0.042 0.141 2266 Planarity : 0.004 0.034 2672 Dihedral : 8.136 77.534 2112 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.68 % Allowed : 10.77 % Favored : 87.55 % 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: 0.33 (0.19), residues: 1832 helix: 1.39 (0.16), residues: 1040 sheet: 0.19 (0.47), residues: 132 loop : -1.74 (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 0.011 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/Z covalent geometry : bond 0.00262 / 0.13 (15804) covalent geometry : angle 0.60858 / 0.31 (21554) hydrogen bonds : bond 0.05490 / 3.74 ( 768) hydrogen bonds : angle 4.42676 / 3.09 ( 2244) Misc. bond : bond 0.00024 / 0.01 ( 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 : 0.559 Fit side-chains REVERT: A 266 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7404 (tpt90) REVERT: A 345 MET cc_start: 0.8625 (mmm) cc_final: 0.8372 (mmm) REVERT: B 266 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7634 (tpt170) REVERT: B 345 MET cc_start: 0.8704 (mmm) cc_final: 0.8367 (mmp) REVERT: C 266 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7397 (tpt90) REVERT: C 345 MET cc_start: 0.8632 (mmm) cc_final: 0.8382 (mmm) REVERT: D 266 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (tpt170) REVERT: D 345 MET cc_start: 0.8701 (mmm) cc_final: 0.8372 (mmp) outliers start: 23 outliers final: 12 residues processed: 194 average time/residue: 0.1334 time to fit residues: 38.0021 Evaluate side-chains 170 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3670 r_free = 0.3670 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113917 restraints weight = 54520.525| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.83 r_work: 0.3057 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 15808 Z= 0.349 Angle : 0.843 9.668 21554 Z= 0.422 Chirality : 0.054 0.204 2266 Planarity : 0.006 0.045 2672 Dihedral : 7.735 80.815 2068 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.18 % Allowed : 12.08 % Favored : 85.74 % 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: -0.40 (0.19), residues: 1832 helix: 0.78 (0.16), residues: 1022 sheet: 0.19 (0.46), residues: 132 loop : -2.00 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 208 TYR 0.018 0.002 TYR A 299 PHE 0.024 0.003 PHE D 100 TRP 0.019 0.002 TRP A 444 HIS 0.011 0.003 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.35 (15804) covalent geometry : angle 0.84284 / 0.42 (21554) hydrogen bonds : bond 0.09785 / 6.63 ( 768) hydrogen bonds : angle 4.93266 / 3.44 ( 2244) Misc. bond : bond 0.00146 / 0.07 ( 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 189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 301 CYS cc_start: 0.7974 (t) cc_final: 0.7148 (m) REVERT: A 447 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.7894 (p90) REVERT: C 119 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7972 (tp) REVERT: C 266 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7554 (tpt90) REVERT: C 301 CYS cc_start: 0.7983 (t) cc_final: 0.7157 (m) REVERT: C 447 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.7896 (p90) outliers start: 31 outliers final: 16 residues processed: 183 average time/residue: 0.1395 time to fit residues: 37.5747 Evaluate side-chains 169 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 122 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3753 r_free = 0.3753 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120733 restraints weight = 62835.990| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.18 r_work: 0.3157 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15808 Z= 0.127 Angle : 0.592 6.603 21554 Z= 0.294 Chirality : 0.042 0.140 2266 Planarity : 0.004 0.035 2672 Dihedral : 7.058 72.696 2064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.56 % Allowed : 13.70 % Favored : 84.74 % 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: 0.26 (0.19), residues: 1832 helix: 1.31 (0.16), residues: 1038 sheet: 0.25 (0.47), residues: 132 loop : -1.72 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.008 0.001 TYR C 47 PHE 0.009 0.001 PHE B 100 TRP 0.015 0.001 TRP C 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15804) covalent geometry : angle 0.59163 / 0.29 (21554) hydrogen bonds : bond 0.05455 / 3.70 ( 768) hydrogen bonds : angle 4.40486 / 3.07 ( 2244) Misc. bond : bond 0.00026 / 0.01 ( 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 189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.601 Fit side-chains REVERT: A 301 CYS cc_start: 0.7686 (t) cc_final: 0.7083 (m) REVERT: A 447 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8175 (p90) REVERT: B 118 LYS cc_start: 0.8109 (mttm) cc_final: 0.7844 (tttp) REVERT: C 266 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7457 (tpt90) REVERT: C 301 CYS cc_start: 0.7705 (t) cc_final: 0.7096 (m) REVERT: C 447 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.8175 (p90) REVERT: D 118 LYS cc_start: 0.8128 (mttm) cc_final: 0.7859 (tttp) outliers start: 21 outliers final: 13 residues processed: 185 average time/residue: 0.1277 time to fit residues: 35.1006 Evaluate side-chains 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3728 r_free = 0.3728 target = 0.149321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118736 restraints weight = 84211.860| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.37 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15808 Z= 0.159 Angle : 0.620 7.451 21554 Z= 0.306 Chirality : 0.043 0.137 2266 Planarity : 0.004 0.035 2672 Dihedral : 7.031 68.750 2064 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.68 % Allowed : 13.82 % 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: 0.35 (0.19), residues: 1832 helix: 1.39 (0.16), residues: 1038 sheet: 0.22 (0.46), residues: 132 loop : -1.67 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.009 0.001 TYR A 299 PHE 0.012 0.002 PHE B 100 TRP 0.012 0.001 TRP A 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15804) covalent geometry : angle 0.62009 / 0.31 (21554) hydrogen bonds : bond 0.06255 / 4.24 ( 768) hydrogen bonds : angle 4.41328 / 3.08 ( 2244) Misc. bond : bond 0.00058 / 0.03 ( 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 189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.580 Fit side-chains REVERT: A 191 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7261 (tt0) REVERT: A 301 CYS cc_start: 0.7686 (t) cc_final: 0.7151 (m) REVERT: A 447 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7935 (p90) REVERT: B 326 ASP cc_start: 0.7189 (m-30) cc_final: 0.6950 (p0) REVERT: C 191 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7270 (tt0) REVERT: C 301 CYS cc_start: 0.7684 (t) cc_final: 0.7148 (m) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.1261 time to fit residues: 34.8378 Evaluate side-chains 175 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 172 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS B 419 GLN D 80 HIS D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116136 restraints weight = 77585.191| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.51 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15808 Z= 0.214 Angle : 0.681 8.778 21554 Z= 0.338 Chirality : 0.046 0.151 2266 Planarity : 0.005 0.037 2672 Dihedral : 7.249 72.762 2064 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.68 % Allowed : 14.32 % Favored : 84.00 % 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: 0.09 (0.19), residues: 1832 helix: 1.21 (0.16), residues: 1034 sheet: 0.07 (0.45), residues: 132 loop : -1.82 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 12 TYR 0.013 0.002 TYR C 299 PHE 0.016 0.002 PHE B 100 TRP 0.015 0.002 TRP C 214 HIS 0.007 0.002 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (15804) covalent geometry : angle 0.68145 / 0.34 (21554) hydrogen bonds : bond 0.07432 / 5.03 ( 768) hydrogen bonds : angle 4.55383 / 3.18 ( 2244) Misc. bond : bond 0.00081 / 0.04 ( 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 180 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.497 Fit side-chains REVERT: A 191 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7269 (tt0) REVERT: A 345 MET cc_start: 0.8359 (mmm) cc_final: 0.7801 (mmm) REVERT: A 447 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7872 (p90) REVERT: B 326 ASP cc_start: 0.7253 (m-30) cc_final: 0.6889 (p0) REVERT: C 191 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7281 (tt0) REVERT: C 345 MET cc_start: 0.8361 (mmm) cc_final: 0.7812 (mmm) REVERT: C 447 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.7887 (p90) REVERT: D 326 ASP cc_start: 0.7279 (m-30) cc_final: 0.6908 (p0) outliers start: 23 outliers final: 21 residues processed: 175 average time/residue: 0.1248 time to fit residues: 33.0920 Evaluate side-chains 176 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 336 THR 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: 0.0020 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 176 optimal weight: 10.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123679 restraints weight = 73531.654| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.48 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2501 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= 0.103 Angle : 0.551 5.931 21554 Z= 0.270 Chirality : 0.040 0.137 2266 Planarity : 0.004 0.032 2672 Dihedral : 6.654 59.632 2064 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 14.69 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1832 helix: 1.74 (0.16), residues: 1036 sheet: 0.10 (0.45), residues: 134 loop : -1.45 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 266 TYR 0.007 0.001 TYR A 47 PHE 0.010 0.001 PHE A 46 TRP 0.015 0.001 TRP B 214 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15804) covalent geometry : angle 0.55141 / 0.27 (21554) hydrogen bonds : bond 0.04188 / 2.83 ( 768) hydrogen bonds : angle 4.24760 / 2.97 ( 2244) Misc. bond : bond 0.00007 / 0.00 ( 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 171 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.429 Fit side-chains REVERT: A 191 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7243 (tt0) REVERT: B 172 TRP cc_start: 0.6058 (t60) cc_final: 0.5764 (t-100) REVERT: B 326 ASP cc_start: 0.7373 (m-30) cc_final: 0.6970 (p0) REVERT: C 191 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7237 (tt0) REVERT: C 447 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8048 (p90) REVERT: D 326 ASP cc_start: 0.7374 (m-30) cc_final: 0.6967 (p0) outliers start: 13 outliers final: 12 residues processed: 169 average time/residue: 0.1266 time to fit residues: 32.0085 Evaluate side-chains 163 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 9 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123047 restraints weight = 70678.375| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.43 r_work: 0.3161 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15808 Z= 0.112 Angle : 0.554 6.026 21554 Z= 0.270 Chirality : 0.041 0.133 2266 Planarity : 0.003 0.031 2672 Dihedral : 6.607 59.910 2062 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.31 % Allowed : 14.32 % 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: 0.94 (0.20), residues: 1832 helix: 1.84 (0.16), residues: 1038 sheet: 0.15 (0.45), residues: 134 loop : -1.30 (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 0.008 0.001 PHE B 100 TRP 0.012 0.001 TRP C 382 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15804) covalent geometry : angle 0.55409 / 0.27 (21554) hydrogen bonds : bond 0.04684 / 3.17 ( 768) hydrogen bonds : angle 4.19900 / 2.94 ( 2244) Misc. bond : bond 0.00033 / 0.02 ( 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 177 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.539 Fit side-chains REVERT: A 191 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7871 (tt0) REVERT: B 118 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7591 (mttm) REVERT: B 172 TRP cc_start: 0.6218 (t60) cc_final: 0.5938 (t-100) REVERT: B 326 ASP cc_start: 0.7686 (m-30) cc_final: 0.6951 (p0) REVERT: C 191 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7881 (tt0) REVERT: C 447 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8352 (p90) REVERT: D 326 ASP cc_start: 0.7677 (m-30) cc_final: 0.6941 (p0) outliers start: 17 outliers final: 12 residues processed: 174 average time/residue: 0.1273 time to fit residues: 33.3124 Evaluate side-chains 162 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 118 LYS 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 7 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 336 THR 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: 7.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118247 restraints weight = 78016.576| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.39 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.005 0.037 15808 Z= 0.224 Angle : 0.690 8.495 21554 Z= 0.342 Chirality : 0.047 0.152 2266 Planarity : 0.005 0.035 2672 Dihedral : 7.107 69.120 2062 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.68 % Allowed : 13.95 % 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: 0.46 (0.20), residues: 1832 helix: 1.48 (0.16), residues: 1022 sheet: 0.19 (0.45), residues: 132 loop : -1.55 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 12 TYR 0.023 0.002 TYR D 299 PHE 0.015 0.002 PHE D 100 TRP 0.015 0.002 TRP C 214 HIS 0.007 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (15804) covalent geometry : angle 0.68959 / 0.34 (21554) hydrogen bonds : bond 0.07360 / 4.97 ( 768) hydrogen bonds : angle 4.50061 / 3.15 ( 2244) Misc. bond : bond 0.00086 / 0.04 ( 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 172 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.533 Fit side-chains REVERT: A 191 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7342 (tt0) REVERT: A 345 MET cc_start: 0.8118 (mmm) cc_final: 0.7647 (mmm) REVERT: B 172 TRP cc_start: 0.5901 (t60) cc_final: 0.5596 (t-100) REVERT: C 191 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7347 (tt0) REVERT: C 345 MET cc_start: 0.8117 (mmm) cc_final: 0.7658 (mmm) REVERT: C 447 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7890 (p90) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.1172 time to fit residues: 30.5735 Evaluate side-chains 166 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 120 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 336 THR Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 178 optimal weight: 0.0010 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124690 restraints weight = 75855.549| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.33 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15808 Z= 0.107 Angle : 0.563 8.484 21554 Z= 0.274 Chirality : 0.041 0.136 2266 Planarity : 0.003 0.031 2672 Dihedral : 6.642 59.830 2062 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 0.88 (0.20), residues: 1832 helix: 1.76 (0.16), residues: 1042 sheet: 0.20 (0.46), residues: 134 loop : -1.31 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 12 TYR 0.023 0.001 TYR D 299 PHE 0.011 0.001 PHE C 46 TRP 0.014 0.001 TRP C 214 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (15804) covalent geometry : angle 0.56305 / 0.27 (21554) hydrogen bonds : bond 0.04356 / 2.94 ( 768) hydrogen bonds : angle 4.23162 / 2.96 ( 2244) Misc. bond : bond 0.00185 / 0.09 ( 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 163 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.523 Fit side-chains REVERT: A 73 ASP cc_start: 0.7783 (t0) cc_final: 0.7581 (m-30) REVERT: A 191 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7286 (tt0) REVERT: B 172 TRP cc_start: 0.6028 (t60) cc_final: 0.5802 (t-100) REVERT: C 73 ASP cc_start: 0.7783 (t0) cc_final: 0.7578 (m-30) REVERT: C 191 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7287 (tt0) REVERT: C 447 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.8078 (p90) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 0.1169 time to fit residues: 28.8416 Evaluate side-chains 156 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120422 restraints weight = 75351.991| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.31 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15808 Z= 0.172 Angle : 0.635 7.909 21554 Z= 0.311 Chirality : 0.044 0.137 2266 Planarity : 0.004 0.032 2672 Dihedral : 6.906 63.493 2062 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.06 % Allowed : 14.82 % Favored : 84.12 % 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: 0.70 (0.20), residues: 1832 helix: 1.59 (0.16), residues: 1042 sheet: 0.16 (0.45), residues: 134 loop : -1.34 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.023 0.001 TYR D 299 PHE 0.012 0.002 PHE D 100 TRP 0.013 0.001 TRP A 214 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (15804) covalent geometry : angle 0.63500 / 0.31 (21554) hydrogen bonds : bond 0.06236 / 4.21 ( 768) hydrogen bonds : angle 4.37431 / 3.06 ( 2244) Misc. bond : bond 0.00109 / 0.05 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.42 seconds wall clock time: 55 minutes 18.75 seconds (3318.75 seconds total)