Starting phenix.real_space_refine on Thu Sep 18 10:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.map" model { file = "/net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6swy_10333/09_2025/6swy_10333.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 10334 2.51 5 N 2682 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16057 Number of models: 1 Model: "" Number of chains: 7 Chain: "5" Number of atoms: 6417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6417 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "8" Number of atoms: 2682 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2676 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 314} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 325, 2676 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 314} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2721 Chain: "1" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3508 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 421} Chain breaks: 7 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "1" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Chain breaks: 4 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "4" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1783 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "9" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 897 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "9" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 4.24, per 1000 atoms: 0.26 Number of scatterers: 16057 At special positions: 0 Unit cell: (122.08, 164.59, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 2970 8.00 N 2682 7.00 C 10334 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=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 777.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 66.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain '5' and resid 6 through 18 Processing helix chain '5' and resid 20 through 27 Processing helix chain '5' and resid 28 through 33 Proline residue: 5 31 - end of helix No H-bonds generated for 'chain '5' and resid 28 through 33' Processing helix chain '5' and resid 34 through 40 removed outlier: 3.891A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 62 Processing helix chain '5' and resid 65 through 73 removed outlier: 4.167A pdb=" N ILE 5 71 " --> pdb=" O GLN 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 74 through 86 Processing helix chain '5' and resid 97 through 115 Processing helix chain '5' and resid 122 through 137 removed outlier: 3.554A pdb=" N LEU 5 126 " --> pdb=" O ASP 5 122 " (cutoff:3.500A) Processing helix chain '5' and resid 144 through 160 Processing helix chain '5' and resid 182 through 205 removed outlier: 4.212A pdb=" N GLN 5 188 " --> pdb=" O THR 5 184 " (cutoff:3.500A) Processing helix chain '5' and resid 206 through 211 removed outlier: 5.337A pdb=" N ASP 5 209 " --> pdb=" O LYS 5 206 " (cutoff:3.500A) Processing helix chain '5' and resid 254 through 272 Processing helix chain '5' and resid 273 through 275 No H-bonds generated for 'chain '5' and resid 273 through 275' Processing helix chain '5' and resid 285 through 295 removed outlier: 3.961A pdb=" N MET 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 317 Proline residue: 5 313 - end of helix Processing helix chain '5' and resid 319 through 322 removed outlier: 3.629A pdb=" N GLU 5 322 " --> pdb=" O LYS 5 319 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 319 through 322' Processing helix chain '5' and resid 323 through 337 removed outlier: 3.691A pdb=" N LEU 5 327 " --> pdb=" O ASP 5 323 " (cutoff:3.500A) Proline residue: 5 332 - end of helix Processing helix chain '5' and resid 348 through 364 removed outlier: 3.531A pdb=" N THR 5 364 " --> pdb=" O TYR 5 360 " (cutoff:3.500A) Processing helix chain '5' and resid 368 through 377 removed outlier: 3.557A pdb=" N THR 5 377 " --> pdb=" O THR 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 378 through 392 removed outlier: 3.652A pdb=" N CYS 5 382 " --> pdb=" O ASN 5 378 " (cutoff:3.500A) Processing helix chain '5' and resid 397 through 416 Processing helix chain '5' and resid 418 through 427 Processing helix chain '5' and resid 430 through 461 removed outlier: 3.930A pdb=" N HIS 5 434 " --> pdb=" O LEU 5 430 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP 5 454 " --> pdb=" O ILE 5 450 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU 5 455 " --> pdb=" O SER 5 451 " (cutoff:3.500A) Processing helix chain '5' and resid 473 through 488 Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 500 through 521 removed outlier: 3.874A pdb=" N ALA 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 525 removed outlier: 3.571A pdb=" N GLY 5 525 " --> pdb=" O TYR 5 522 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 522 through 525' Processing helix chain '5' and resid 529 through 547 removed outlier: 4.451A pdb=" N ASN 5 545 " --> pdb=" O GLY 5 541 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE 5 546 " --> pdb=" O SER 5 542 " (cutoff:3.500A) Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 561 through 571 removed outlier: 4.047A pdb=" N ILE 5 565 " --> pdb=" O GLY 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 585 through 593 Processing helix chain '5' and resid 598 through 612 Processing helix chain '5' and resid 616 through 627 Processing helix chain '5' and resid 628 through 634 Processing helix chain '5' and resid 640 through 656 Processing helix chain '5' and resid 658 through 668 removed outlier: 3.752A pdb=" N VAL 5 662 " --> pdb=" O SER 5 658 " (cutoff:3.500A) Processing helix chain '5' and resid 690 through 702 Processing helix chain '5' and resid 706 through 725 Processing helix chain '5' and resid 727 through 737 removed outlier: 3.838A pdb=" N GLN 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) Processing helix chain '5' and resid 738 through 749 Processing helix chain '5' and resid 761 through 777 Processing helix chain '5' and resid 874 through 886 removed outlier: 3.666A pdb=" N GLU 5 878 " --> pdb=" O ARG 5 874 " (cutoff:3.500A) Processing helix chain '5' and resid 887 through 895 removed outlier: 3.614A pdb=" N LEU 5 891 " --> pdb=" O GLY 5 887 " (cutoff:3.500A) Processing helix chain '5' and resid 896 through 898 No H-bonds generated for 'chain '5' and resid 896 through 898' Processing helix chain '5' and resid 900 through 918 Processing helix chain '8' and resid 35 through 53 removed outlier: 3.986A pdb=" N TYR 8 46 " --> pdb=" O GLN 8 42 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA 8 48 " --> pdb=" O ALA 8 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET 8 49 " --> pdb=" O LYS 8 45 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY 8 50 " --> pdb=" O TYR 8 46 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU 8 51 " --> pdb=" O SER 8 47 " (cutoff:3.500A) Processing helix chain '8' and resid 88 through 100 Processing helix chain '8' and resid 102 through 114 Processing helix chain '8' and resid 118 through 130 Processing helix chain '8' and resid 130 through 143 Processing helix chain '8' and resid 145 through 157 Processing helix chain '8' and resid 193 through 211 Processing helix chain '8' and resid 220 through 234 Processing helix chain '8' and resid 234 through 240 removed outlier: 3.993A pdb=" N SER 8 240 " --> pdb=" O ILE 8 236 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 257 Processing helix chain '8' and resid 273 through 278 Processing helix chain '8' and resid 280 through 308 removed outlier: 3.649A pdb=" N SER 8 284 " --> pdb=" O ILE 8 280 " (cutoff:3.500A) Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 352 through 356 Processing helix chain '8' and resid 394 through 401 removed outlier: 4.376A pdb=" N GLU 8 401 " --> pdb=" O ASN 8 397 " (cutoff:3.500A) Processing helix chain '8' and resid 417 through 423 Processing helix chain '8' and resid 427 through 446 removed outlier: 3.626A pdb=" N GLN 8 431 " --> pdb=" O PRO 8 427 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 17 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 26 through 37 Processing helix chain '1' and resid 38 through 41 Processing helix chain '1' and resid 70 through 81 Processing helix chain '1' and resid 107 through 116 removed outlier: 3.555A pdb=" N PHE 1 111 " --> pdb=" O ASP 1 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR 1 112 " --> pdb=" O VAL 1 108 " (cutoff:3.500A) Processing helix chain '1' and resid 317 through 321 Processing helix chain '1' and resid 497 through 504 Processing helix chain '1' and resid 596 through 613 removed outlier: 3.548A pdb=" N TYR 1 600 " --> pdb=" O ASP 1 596 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS 1 603 " --> pdb=" O GLY 1 599 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP 1 604 " --> pdb=" O TYR 1 600 " (cutoff:3.500A) Processing helix chain '1' and resid 708 through 725 removed outlier: 3.733A pdb=" N ASN 1 712 " --> pdb=" O GLY 1 708 " (cutoff:3.500A) Processing helix chain '1' and resid 727 through 742 Processing helix chain '1' and resid 752 through 781 Processing helix chain '1' and resid 914 through 932 removed outlier: 3.518A pdb=" N THR 1 922 " --> pdb=" O VAL 1 918 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG 1 923 " --> pdb=" O ILE 1 919 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 1 927 " --> pdb=" O ARG 1 923 " (cutoff:3.500A) Processing helix chain '1' and resid 944 through 949 removed outlier: 3.524A pdb=" N LYS 1 947 " --> pdb=" O ARG 1 944 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE 1 949 " --> pdb=" O TYR 1 946 " (cutoff:3.500A) Processing helix chain '1' and resid 950 through 955 Processing helix chain '1' and resid 3786 through 3799 Processing helix chain '1' and resid 3810 through 3827 removed outlier: 4.358A pdb=" N UNK 13814 " --> pdb=" O UNK 13810 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N UNK 13816 " --> pdb=" O UNK 13812 " (cutoff:3.500A) Processing helix chain '1' and resid 3837 through 3849 removed outlier: 4.260A pdb=" N UNK 13843 " --> pdb=" O UNK 13839 " (cutoff:3.500A) Processing helix chain '1' and resid 3856 through 3880 removed outlier: 3.711A pdb=" N UNK 13865 " --> pdb=" O UNK 13861 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK 13874 " --> pdb=" O UNK 13870 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK 13877 " --> pdb=" O UNK 13873 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N UNK 13878 " --> pdb=" O UNK 13874 " (cutoff:3.500A) Processing helix chain '1' and resid 3891 through 3908 Processing helix chain '4' and resid 92 through 97 Processing helix chain '4' and resid 205 through 209 removed outlier: 4.307A pdb=" N GLU 4 208 " --> pdb=" O VAL 4 205 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE 4 209 " --> pdb=" O LEU 4 206 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 205 through 209' Processing helix chain '4' and resid 212 through 221 Processing helix chain '4' and resid 223 through 230 removed outlier: 3.722A pdb=" N PHE 4 230 " --> pdb=" O PHE 4 226 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 277 removed outlier: 4.320A pdb=" N LYS 4 277 " --> pdb=" O PHE 4 273 " (cutoff:3.500A) Processing helix chain '9' and resid 224 through 240 removed outlier: 3.768A pdb=" N VAL 9 240 " --> pdb=" O GLU 9 236 " (cutoff:3.500A) Processing helix chain '9' and resid 243 through 254 Processing helix chain '9' and resid 261 through 279 removed outlier: 3.662A pdb=" N LEU 9 265 " --> pdb=" O ASN 9 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 9 273 " --> pdb=" O SER 9 269 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS 9 276 " --> pdb=" O LEU 9 272 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR 9 277 " --> pdb=" O ILE 9 273 " (cutoff:3.500A) Processing helix chain '9' and resid 304 through 314 Processing helix chain '9' and resid 345 through 350 Processing helix chain '9' and resid 352 through 371 removed outlier: 3.765A pdb=" N TRP 9 356 " --> pdb=" O ASP 9 352 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR 9 371 " --> pdb=" O PHE 9 367 " (cutoff:3.500A) Processing helix chain '9' and resid 3188 through 3199 Processing helix chain '9' and resid 3205 through 3215 Processing helix chain '9' and resid 3292 through 3298 removed outlier: 3.927A pdb=" N UNK 93296 " --> pdb=" O UNK 93292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 214 through 218 Processing sheet with id=AA2, first strand: chain '8' and resid 32 through 33 removed outlier: 7.040A pdb=" N LYS 8 32 " --> pdb=" O GLY 8 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain '1' and resid 386 through 389 Processing sheet with id=AA5, first strand: chain '1' and resid 557 through 564 removed outlier: 5.553A pdb=" N HIS 1 558 " --> pdb=" O LYS 1 554 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS 1 554 " --> pdb=" O HIS 1 558 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY 1 560 " --> pdb=" O PHE 1 552 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE 1 552 " --> pdb=" O GLY 1 560 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE 1 550 " --> pdb=" O ALA 1 562 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER 1 582 " --> pdb=" O LEU 1 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 687 through 688 Processing sheet with id=AA7, first strand: chain '4' and resid 128 through 135 removed outlier: 3.887A pdb=" N GLN 4 141 " --> pdb=" O ARG 4 170 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER 4 164 " --> pdb=" O LYS 4 147 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2591 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: 2.81 Time building geometry restraints manager: 1.76 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: 5150 1.34 - 1.46: 2703 1.46 - 1.58: 8400 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 16361 Sorted by residual: bond pdb=" C ASP 4 150 " pdb=" N LEU 4 151 " ideal model delta sigma weight residual 1.331 1.287 0.044 2.07e-02 2.33e+03 4.49e+00 bond pdb=" CG1 ILE 1 612 " pdb=" CD1 ILE 1 612 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" C LYS 9 239 " pdb=" N VAL 9 240 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.24e-02 6.50e+03 2.13e+00 bond pdb=" CG1 ILE 8 146 " pdb=" CD1 ILE 8 146 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.19e+00 bond pdb=" CG PRO 8 424 " pdb=" CD PRO 8 424 " ideal model delta sigma weight residual 1.503 1.471 0.032 3.40e-02 8.65e+02 8.99e-01 ... (remaining 16356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 21612 1.73 - 3.46: 449 3.46 - 5.20: 52 5.20 - 6.93: 15 6.93 - 8.66: 2 Bond angle restraints: 22130 Sorted by residual: angle pdb=" C GLY 1 534 " pdb=" N ARG 1 535 " pdb=" CA ARG 1 535 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C LYS 4 191 " pdb=" N GLU 4 192 " pdb=" CA GLU 4 192 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N ALA 5 30 " pdb=" CA ALA 5 30 " pdb=" C ALA 5 30 " ideal model delta sigma weight residual 109.81 116.25 -6.44 2.21e+00 2.05e-01 8.50e+00 angle pdb=" N GLU 8 103 " pdb=" CA GLU 8 103 " pdb=" C GLU 8 103 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.72e+00 angle pdb=" C ASN 4 189 " pdb=" N HIS 4 190 " pdb=" CA HIS 4 190 " ideal model delta sigma weight residual 121.54 126.41 -4.87 1.91e+00 2.74e-01 6.50e+00 ... (remaining 22125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8950 17.84 - 35.68: 745 35.68 - 53.53: 113 53.53 - 71.37: 26 71.37 - 89.21: 18 Dihedral angle restraints: 9852 sinusoidal: 3828 harmonic: 6024 Sorted by residual: dihedral pdb=" CA VAL 4 108 " pdb=" C VAL 4 108 " pdb=" N ILE 4 109 " pdb=" CA ILE 4 109 " ideal model delta harmonic sigma weight residual 180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA LEU 5 29 " pdb=" C LEU 5 29 " pdb=" N ALA 5 30 " pdb=" CA ALA 5 30 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1527 0.031 - 0.062: 659 0.062 - 0.092: 225 0.092 - 0.123: 103 0.123 - 0.154: 14 Chirality restraints: 2528 Sorted by residual: chirality pdb=" CA ILE 5 627 " pdb=" N ILE 5 627 " pdb=" C ILE 5 627 " pdb=" CB ILE 5 627 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE 4 327 " pdb=" N ILE 4 327 " pdb=" C ILE 4 327 " pdb=" CB ILE 4 327 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE 4 169 " pdb=" N ILE 4 169 " pdb=" C ILE 4 169 " pdb=" CB ILE 4 169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 2525 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP 5 606 " 0.033 2.00e-02 2.50e+03 3.20e-02 2.55e+01 pdb=" CG TRP 5 606 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP 5 606 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP 5 606 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 5 606 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP 5 606 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP 5 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP 5 606 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 5 606 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP 5 606 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 124 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO 4 125 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO 4 125 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 4 125 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 572 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO 1 573 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 1 573 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 1 573 " 0.028 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1487 2.74 - 3.28: 15566 3.28 - 3.82: 25009 3.82 - 4.36: 30120 4.36 - 4.90: 53526 Nonbonded interactions: 125708 Sorted by model distance: nonbonded pdb=" O ASN 8 276 " pdb=" OG SER 8 279 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR 5 515 " pdb=" OD2 ASP 5 572 " model vdw 2.224 3.040 nonbonded pdb=" ND2 ASN 5 109 " pdb=" OE1 GLU 5 153 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG 8 207 " pdb=" O TYR 8 278 " model vdw 2.244 3.120 nonbonded pdb=" O ARG 1 10 " pdb=" ND2 ASN 1 14 " model vdw 2.246 3.120 ... (remaining 125703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16361 Z= 0.184 Angle : 0.622 8.662 22130 Z= 0.346 Chirality : 0.042 0.154 2528 Planarity : 0.004 0.061 2804 Dihedral : 13.996 89.211 5912 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % 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 aren not related in a simple way. whole: 0.07 (0.20), residues: 1821 helix: 1.20 (0.16), residues: 1029 sheet: 0.34 (0.47), residues: 132 loop : -1.93 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 8 117 TYR 0.014 0.002 TYR 5 84 PHE 0.015 0.002 PHE 1 515 TRP 0.084 0.002 TRP 5 606 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00433 (16361) covalent geometry : angle 0.62209 (22130) hydrogen bonds : bond 0.08435 ( 879) hydrogen bonds : angle 4.78360 ( 2591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.766 Fit side-chains REVERT: 5 473 ASP cc_start: 0.7357 (t0) cc_final: 0.7067 (t70) REVERT: 1 502 LYS cc_start: 0.8831 (tttm) cc_final: 0.8631 (tttm) REVERT: 4 284 ASN cc_start: 0.8217 (t0) cc_final: 0.7873 (t0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1544 time to fit residues: 42.1370 Evaluate side-chains 160 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 272 HIS 5 434 HIS 5 598 HIS ** 1 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103951 restraints weight = 31346.079| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.85 r_work: 0.2753 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16361 Z= 0.140 Angle : 0.537 9.030 22130 Z= 0.281 Chirality : 0.040 0.145 2528 Planarity : 0.004 0.058 2804 Dihedral : 4.405 25.009 2153 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.82 % Allowed : 5.34 % Favored : 93.84 % 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 aren not related in a simple way. whole: 0.58 (0.20), residues: 1821 helix: 1.62 (0.16), residues: 1034 sheet: 0.60 (0.47), residues: 131 loop : -1.77 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 117 TYR 0.014 0.001 TYR 1 103 PHE 0.025 0.001 PHE 1 515 TRP 0.035 0.001 TRP 5 606 HIS 0.004 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00335 (16361) covalent geometry : angle 0.53713 (22130) hydrogen bonds : bond 0.04495 ( 879) hydrogen bonds : angle 4.27548 ( 2591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.677 Fit side-chains REVERT: 5 584 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8279 (m110) REVERT: 8 227 ILE cc_start: 0.8928 (mt) cc_final: 0.8587 (mp) REVERT: 1 502 LYS cc_start: 0.9132 (tttm) cc_final: 0.8907 (tttm) REVERT: 1 535 ARG cc_start: 0.7704 (tmm160) cc_final: 0.7358 (tpt170) REVERT: 4 284 ASN cc_start: 0.8407 (t0) cc_final: 0.7937 (t0) REVERT: 9 234 TYR cc_start: 0.7023 (t80) cc_final: 0.6645 (t80) REVERT: 9 310 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8238 (tm-30) outliers start: 13 outliers final: 8 residues processed: 176 average time/residue: 0.1453 time to fit residues: 37.8190 Evaluate side-chains 167 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 743 ILE Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 95 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 447 GLN ** 1 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106621 restraints weight = 30845.728| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.66 r_work: 0.2721 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16361 Z= 0.142 Angle : 0.519 8.932 22130 Z= 0.272 Chirality : 0.039 0.146 2528 Planarity : 0.004 0.054 2804 Dihedral : 4.274 23.148 2153 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.23 % Allowed : 6.92 % Favored : 91.84 % 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 aren not related in a simple way. whole: 0.84 (0.20), residues: 1821 helix: 1.83 (0.17), residues: 1035 sheet: 0.71 (0.46), residues: 132 loop : -1.65 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 117 TYR 0.012 0.001 TYR 9 234 PHE 0.021 0.001 PHE 1 515 TRP 0.026 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00343 (16361) covalent geometry : angle 0.51879 (22130) hydrogen bonds : bond 0.04448 ( 879) hydrogen bonds : angle 4.20311 ( 2591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.806 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8872 (mt) cc_final: 0.8546 (mp) REVERT: 1 502 LYS cc_start: 0.9079 (tttm) cc_final: 0.8842 (tttm) REVERT: 1 535 ARG cc_start: 0.7752 (tmm160) cc_final: 0.7298 (tpt170) REVERT: 4 191 LYS cc_start: 0.7878 (pttt) cc_final: 0.7558 (ptpp) REVERT: 4 284 ASN cc_start: 0.8403 (t0) cc_final: 0.7905 (t0) outliers start: 19 outliers final: 17 residues processed: 177 average time/residue: 0.1541 time to fit residues: 39.8440 Evaluate side-chains 176 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 188 GLN 1 581 ASN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105409 restraints weight = 23011.911| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.93 r_work: 0.2817 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16361 Z= 0.146 Angle : 0.516 9.577 22130 Z= 0.270 Chirality : 0.039 0.148 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.228 22.546 2153 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.58 % Allowed : 8.63 % Favored : 89.79 % 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 aren not related in a simple way. whole: 0.93 (0.20), residues: 1821 helix: 1.90 (0.17), residues: 1036 sheet: 0.73 (0.46), residues: 132 loop : -1.59 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 117 TYR 0.011 0.001 TYR 5 333 PHE 0.020 0.001 PHE 1 515 TRP 0.016 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00357 (16361) covalent geometry : angle 0.51580 (22130) hydrogen bonds : bond 0.04458 ( 879) hydrogen bonds : angle 4.17629 ( 2591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.596 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: 8 192 ASP cc_start: 0.8026 (p0) cc_final: 0.7824 (p0) REVERT: 8 227 ILE cc_start: 0.8987 (mt) cc_final: 0.8658 (mp) REVERT: 1 502 LYS cc_start: 0.9134 (tttm) cc_final: 0.8919 (tttm) REVERT: 1 535 ARG cc_start: 0.7854 (tmm160) cc_final: 0.7334 (tpt170) REVERT: 4 284 ASN cc_start: 0.8446 (t0) cc_final: 0.7947 (t0) outliers start: 25 outliers final: 19 residues processed: 177 average time/residue: 0.1446 time to fit residues: 37.7697 Evaluate side-chains 180 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 497 ILE Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 280 ASP Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 102 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 139 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 237 ASN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104301 restraints weight = 31569.242| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.05 r_work: 0.2736 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16361 Z= 0.106 Angle : 0.476 10.642 22130 Z= 0.249 Chirality : 0.038 0.141 2528 Planarity : 0.003 0.050 2804 Dihedral : 3.994 20.198 2153 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.64 % Allowed : 9.21 % Favored : 89.14 % 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 aren not related in a simple way. whole: 1.18 (0.20), residues: 1821 helix: 2.09 (0.17), residues: 1036 sheet: 0.81 (0.46), residues: 132 loop : -1.47 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.011 0.001 TYR 5 360 PHE 0.019 0.001 PHE 1 515 TRP 0.009 0.001 TRP 5 606 HIS 0.003 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00242 (16361) covalent geometry : angle 0.47640 (22130) hydrogen bonds : bond 0.03648 ( 879) hydrogen bonds : angle 4.00835 ( 2591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.592 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: 8 49 MET cc_start: 0.8157 (mmm) cc_final: 0.7881 (mmm) REVERT: 8 227 ILE cc_start: 0.8959 (mt) cc_final: 0.8617 (mp) REVERT: 1 502 LYS cc_start: 0.9104 (tttm) cc_final: 0.8881 (tttm) REVERT: 1 535 ARG cc_start: 0.7743 (tmm160) cc_final: 0.7270 (tmm-80) REVERT: 4 284 ASN cc_start: 0.8434 (t0) cc_final: 0.7944 (t0) REVERT: 4 300 ASP cc_start: 0.6747 (t70) cc_final: 0.6500 (t70) REVERT: 9 310 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8342 (tm-30) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.1360 time to fit residues: 39.9760 Evaluate side-chains 181 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 102 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106602 restraints weight = 29395.164| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.75 r_work: 0.2760 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16361 Z= 0.111 Angle : 0.481 10.268 22130 Z= 0.251 Chirality : 0.038 0.140 2528 Planarity : 0.003 0.049 2804 Dihedral : 3.962 19.971 2153 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.82 % Allowed : 9.45 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.21), residues: 1821 helix: 2.14 (0.17), residues: 1038 sheet: 0.90 (0.47), residues: 132 loop : -1.41 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.010 0.001 TYR 5 333 PHE 0.019 0.001 PHE 1 515 TRP 0.008 0.001 TRP 5 606 HIS 0.004 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00258 (16361) covalent geometry : angle 0.48086 (22130) hydrogen bonds : bond 0.03730 ( 879) hydrogen bonds : angle 3.98614 ( 2591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.576 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: 8 192 ASP cc_start: 0.7878 (p0) cc_final: 0.7618 (p0) REVERT: 8 227 ILE cc_start: 0.8895 (mt) cc_final: 0.8553 (mp) REVERT: 1 502 LYS cc_start: 0.9065 (tttm) cc_final: 0.8834 (tttm) REVERT: 1 535 ARG cc_start: 0.7684 (tmm160) cc_final: 0.7275 (tmm-80) REVERT: 4 284 ASN cc_start: 0.8390 (t0) cc_final: 0.7865 (t0) outliers start: 29 outliers final: 24 residues processed: 178 average time/residue: 0.1188 time to fit residues: 31.9505 Evaluate side-chains 184 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.103008 restraints weight = 29189.192| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.17 r_work: 0.2694 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16361 Z= 0.221 Angle : 0.584 11.477 22130 Z= 0.302 Chirality : 0.042 0.161 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.403 22.456 2153 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.94 % Allowed : 9.80 % Favored : 88.26 % 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 aren not related in a simple way. whole: 0.91 (0.20), residues: 1821 helix: 1.86 (0.16), residues: 1037 sheet: 0.68 (0.46), residues: 134 loop : -1.56 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 244 TYR 0.015 0.002 TYR 9 234 PHE 0.022 0.002 PHE 1 515 TRP 0.012 0.001 TRP 5 606 HIS 0.006 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00559 (16361) covalent geometry : angle 0.58427 (22130) hydrogen bonds : bond 0.05509 ( 879) hydrogen bonds : angle 4.30347 ( 2591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.499 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8931 (mt) cc_final: 0.8600 (mp) REVERT: 1 502 LYS cc_start: 0.9060 (tttm) cc_final: 0.8827 (tttm) REVERT: 4 284 ASN cc_start: 0.8386 (t0) cc_final: 0.7886 (t0) REVERT: 9 310 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8329 (tm-30) outliers start: 31 outliers final: 26 residues processed: 179 average time/residue: 0.1459 time to fit residues: 38.8607 Evaluate side-chains 182 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 743 ILE Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 295 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 497 ILE Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 553 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 709 SER Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108846 restraints weight = 30845.864| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.17 r_work: 0.2763 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16361 Z= 0.111 Angle : 0.491 12.331 22130 Z= 0.256 Chirality : 0.038 0.142 2528 Planarity : 0.003 0.051 2804 Dihedral : 4.047 19.850 2153 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.58 % Allowed : 10.39 % Favored : 88.03 % 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 aren not related in a simple way. whole: 1.24 (0.20), residues: 1821 helix: 2.11 (0.17), residues: 1038 sheet: 0.82 (0.47), residues: 133 loop : -1.40 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.013 0.001 TYR 9 234 PHE 0.019 0.001 PHE 1 515 TRP 0.008 0.001 TRP 4 220 HIS 0.003 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00255 (16361) covalent geometry : angle 0.49105 (22130) hydrogen bonds : bond 0.03756 ( 879) hydrogen bonds : angle 4.02969 ( 2591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.671 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: 8 227 ILE cc_start: 0.8933 (mt) cc_final: 0.8595 (mp) REVERT: 1 502 LYS cc_start: 0.9096 (tttm) cc_final: 0.8874 (tttm) REVERT: 4 284 ASN cc_start: 0.8419 (t0) cc_final: 0.7922 (t0) REVERT: 9 310 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 25 outliers final: 23 residues processed: 176 average time/residue: 0.1407 time to fit residues: 37.0145 Evaluate side-chains 180 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102274 restraints weight = 25561.661| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.29 r_work: 0.2791 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16361 Z= 0.143 Angle : 0.518 12.490 22130 Z= 0.268 Chirality : 0.039 0.148 2528 Planarity : 0.003 0.051 2804 Dihedral : 4.106 20.599 2153 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.82 % Allowed : 10.45 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1821 helix: 2.09 (0.16), residues: 1038 sheet: 0.86 (0.47), residues: 132 loop : -1.46 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.013 0.001 TYR 9 234 PHE 0.020 0.001 PHE 1 515 TRP 0.008 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00350 (16361) covalent geometry : angle 0.51795 (22130) hydrogen bonds : bond 0.04334 ( 879) hydrogen bonds : angle 4.09007 ( 2591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.661 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: 8 227 ILE cc_start: 0.9026 (mt) cc_final: 0.8704 (mp) REVERT: 1 502 LYS cc_start: 0.9185 (tttm) cc_final: 0.8977 (tttm) REVERT: 4 284 ASN cc_start: 0.8537 (t0) cc_final: 0.8066 (t0) outliers start: 29 outliers final: 26 residues processed: 175 average time/residue: 0.1342 time to fit residues: 35.0297 Evaluate side-chains 181 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 152 GLU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 225 SER Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 101 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 0.0570 chunk 94 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 172 optimal weight: 0.0570 chunk 158 optimal weight: 20.0000 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109883 restraints weight = 23300.224| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.84 r_work: 0.2886 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16361 Z= 0.095 Angle : 0.475 12.820 22130 Z= 0.246 Chirality : 0.037 0.143 2528 Planarity : 0.003 0.049 2804 Dihedral : 3.837 19.044 2153 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.58 % Allowed : 10.74 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.21), residues: 1821 helix: 2.28 (0.17), residues: 1038 sheet: 0.88 (0.47), residues: 132 loop : -1.30 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.012 0.001 TYR 9 234 PHE 0.019 0.001 PHE 1 515 TRP 0.006 0.001 TRP 5 777 HIS 0.002 0.000 HIS 1 558 Details of bonding type rmsd covalent geometry : bond 0.00207 (16361) covalent geometry : angle 0.47521 (22130) hydrogen bonds : bond 0.03216 ( 879) hydrogen bonds : angle 3.90086 ( 2591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.531 Fit side-chains REVERT: 5 67 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: 8 227 ILE cc_start: 0.8936 (mt) cc_final: 0.8595 (mp) REVERT: 1 502 LYS cc_start: 0.9128 (tttm) cc_final: 0.8914 (tttm) REVERT: 4 284 ASN cc_start: 0.8416 (t0) cc_final: 0.7925 (t0) outliers start: 25 outliers final: 22 residues processed: 180 average time/residue: 0.1225 time to fit residues: 33.7589 Evaluate side-chains 184 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 85 ILE Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 57 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107866 restraints weight = 31165.635| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.66 r_work: 0.2793 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16361 Z= 0.093 Angle : 0.470 12.434 22130 Z= 0.243 Chirality : 0.037 0.143 2528 Planarity : 0.003 0.045 2804 Dihedral : 3.701 18.612 2153 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.47 % Allowed : 10.97 % Favored : 87.56 % 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 aren not related in a simple way. whole: 1.57 (0.21), residues: 1821 helix: 2.36 (0.17), residues: 1041 sheet: 0.92 (0.47), residues: 132 loop : -1.22 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 893 TYR 0.012 0.001 TYR 9 234 PHE 0.018 0.001 PHE 1 515 TRP 0.006 0.001 TRP 4 220 HIS 0.003 0.001 HIS 5 474 Details of bonding type rmsd covalent geometry : bond 0.00206 (16361) covalent geometry : angle 0.47004 (22130) hydrogen bonds : bond 0.03142 ( 879) hydrogen bonds : angle 3.84546 ( 2591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4406.73 seconds wall clock time: 76 minutes 7.03 seconds (4567.03 seconds total)