Starting phenix.real_space_refine on Fri Sep 27 12:53:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_10333.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_10333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_10333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_10333.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/09_2024/6swy_10333.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'TYR:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS: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, 'TYR:plan': 2, 'ASP:plan': 1} 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: 10.40, per 1000 atoms: 0.65 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: 4.10 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.62 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: 5.06 Time building geometry restraints manager: 4.76 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: 1.640 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- 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= 0.274 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 : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.084 0.002 TRP 5 606 HIS 0.006 0.001 HIS 5 272 PHE 0.015 0.002 PHE 1 515 TYR 0.014 0.002 TYR 5 84 ARG 0.009 0.001 ARG 8 117 *********************** 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 fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.711 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: 0.3112 time to fit residues: 84.6149 Evaluate side-chains 160 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16361 Z= 0.295 Angle : 0.579 8.882 22130 Z= 0.302 Chirality : 0.042 0.153 2528 Planarity : 0.004 0.061 2804 Dihedral : 4.587 26.449 2153 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.00 % Allowed : 5.40 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1821 helix: 1.47 (0.16), residues: 1034 sheet: 0.53 (0.46), residues: 131 loop : -1.83 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 5 606 HIS 0.006 0.001 HIS 5 474 PHE 0.024 0.002 PHE 1 515 TYR 0.015 0.001 TYR 1 103 ARG 0.006 0.000 ARG 8 117 *********************** 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 181 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.723 Fit side-chains REVERT: 5 584 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8240 (m110) REVERT: 8 227 ILE cc_start: 0.8969 (mt) cc_final: 0.8604 (mp) REVERT: 4 284 ASN cc_start: 0.8202 (t0) cc_final: 0.7692 (t0) REVERT: 9 234 TYR cc_start: 0.7332 (t80) cc_final: 0.6927 (t80) REVERT: 9 310 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7947 (tm-30) outliers start: 16 outliers final: 11 residues processed: 173 average time/residue: 0.3084 time to fit residues: 78.1248 Evaluate side-chains 165 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 409 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 280 ASP 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 99 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 447 GLN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16361 Z= 0.299 Angle : 0.564 9.114 22130 Z= 0.294 Chirality : 0.041 0.154 2528 Planarity : 0.004 0.058 2804 Dihedral : 4.514 24.996 2153 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.23 % Allowed : 7.69 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1821 helix: 1.61 (0.16), residues: 1034 sheet: 0.63 (0.47), residues: 131 loop : -1.76 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 5 606 HIS 0.006 0.001 HIS 5 474 PHE 0.022 0.002 PHE 1 515 TYR 0.013 0.002 TYR 9 234 ARG 0.005 0.000 ARG 8 117 *********************** 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 182 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.967 Fit side-chains REVERT: 5 584 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8221 (m110) REVERT: 8 227 ILE cc_start: 0.8974 (mt) cc_final: 0.8602 (mp) REVERT: 4 191 LYS cc_start: 0.7847 (pttt) cc_final: 0.7370 (ptpp) REVERT: 4 284 ASN cc_start: 0.8117 (t0) cc_final: 0.7612 (t0) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.3189 time to fit residues: 81.5612 Evaluate side-chains 175 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 534 MET 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 289 LEU 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 272 ILE Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 280 ASP 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 177 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 188 GLN 5 598 HIS ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 581 ASN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0866 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= 0.227 Angle : 0.521 9.690 22130 Z= 0.273 Chirality : 0.039 0.146 2528 Planarity : 0.004 0.055 2804 Dihedral : 4.311 23.028 2153 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.70 % Allowed : 8.98 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1821 helix: 1.82 (0.17), residues: 1036 sheet: 0.71 (0.47), residues: 132 loop : -1.65 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 PHE 0.021 0.001 PHE 1 515 TYR 0.012 0.001 TYR 9 234 ARG 0.005 0.000 ARG 8 117 *********************** 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 192 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.825 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8974 (mt) cc_final: 0.8621 (mp) REVERT: 4 284 ASN cc_start: 0.8216 (t0) cc_final: 0.7711 (t0) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.2878 time to fit residues: 77.3583 Evaluate side-chains 173 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 380 ILE 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 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 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 280 ASP Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 163 optimal weight: 0.0170 chunk 132 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- 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** 4 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16361 Z= 0.210 Angle : 0.511 10.373 22130 Z= 0.267 Chirality : 0.039 0.146 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.208 21.944 2153 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.88 % Allowed : 9.98 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1821 helix: 1.92 (0.17), residues: 1037 sheet: 0.74 (0.47), residues: 132 loop : -1.57 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 PHE 0.019 0.001 PHE 1 515 TYR 0.011 0.001 TYR 9 234 ARG 0.004 0.000 ARG 5 893 *********************** 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 192 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 2.210 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8983 (mt) cc_final: 0.8619 (mp) REVERT: 1 535 ARG cc_start: 0.7495 (tmm160) cc_final: 0.7127 (tpt170) REVERT: 4 284 ASN cc_start: 0.8238 (t0) cc_final: 0.7718 (t0) outliers start: 30 outliers final: 26 residues processed: 179 average time/residue: 0.3171 time to fit residues: 83.4039 Evaluate side-chains 181 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 380 ILE 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 295 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 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 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 155 ASP Chi-restraints excluded: chain 4 residue 225 SER Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 280 ASP 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 64 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16361 Z= 0.221 Angle : 0.514 10.663 22130 Z= 0.268 Chirality : 0.039 0.147 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.182 21.128 2153 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.05 % Allowed : 10.04 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1821 helix: 1.96 (0.16), residues: 1037 sheet: 0.70 (0.46), residues: 133 loop : -1.54 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 606 HIS 0.005 0.001 HIS 5 474 PHE 0.019 0.001 PHE 1 515 TYR 0.011 0.001 TYR 5 333 ARG 0.005 0.000 ARG 5 893 *********************** 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 193 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.995 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8967 (mt) cc_final: 0.8602 (mp) REVERT: 4 284 ASN cc_start: 0.8234 (t0) cc_final: 0.7711 (t0) REVERT: 9 310 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7988 (tm-30) outliers start: 33 outliers final: 30 residues processed: 182 average time/residue: 0.2866 time to fit residues: 78.4354 Evaluate side-chains 182 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 380 ILE 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 289 LEU Chi-restraints excluded: chain 8 residue 295 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 383 VAL Chi-restraints excluded: chain 1 residue 400 THR 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 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 155 ASP Chi-restraints excluded: chain 4 residue 225 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1122 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= 0.209 Angle : 0.509 11.418 22130 Z= 0.265 Chirality : 0.039 0.145 2528 Planarity : 0.003 0.052 2804 Dihedral : 4.133 20.475 2153 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.05 % Allowed : 10.50 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1821 helix: 2.02 (0.16), residues: 1037 sheet: 0.74 (0.46), residues: 133 loop : -1.49 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 4 220 HIS 0.004 0.001 HIS 5 474 PHE 0.020 0.001 PHE 1 515 TYR 0.011 0.001 TYR 5 333 ARG 0.005 0.000 ARG 5 893 *********************** 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 190 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.858 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8965 (mt) cc_final: 0.8599 (mp) REVERT: 4 284 ASN cc_start: 0.8243 (t0) cc_final: 0.7719 (t0) outliers start: 33 outliers final: 30 residues processed: 178 average time/residue: 0.2714 time to fit residues: 73.5077 Evaluate side-chains 183 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 534 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 289 LEU Chi-restraints excluded: chain 8 residue 295 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 383 VAL Chi-restraints excluded: chain 1 residue 400 THR 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 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 155 ASP 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 118 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16361 Z= 0.227 Angle : 0.520 12.191 22130 Z= 0.270 Chirality : 0.039 0.147 2528 Planarity : 0.003 0.052 2804 Dihedral : 4.168 20.648 2153 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.11 % Allowed : 10.62 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1821 helix: 2.01 (0.16), residues: 1037 sheet: 0.80 (0.46), residues: 132 loop : -1.51 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 777 HIS 0.005 0.001 HIS 5 474 PHE 0.021 0.001 PHE 1 515 TYR 0.011 0.001 TYR 5 333 ARG 0.005 0.000 ARG 5 893 *********************** 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 190 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.862 Fit side-chains REVERT: 5 244 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7623 (ttm170) REVERT: 8 227 ILE cc_start: 0.8966 (mt) cc_final: 0.8599 (mp) REVERT: 4 191 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7573 (mtmt) REVERT: 4 284 ASN cc_start: 0.8276 (t0) cc_final: 0.7767 (t0) REVERT: 9 250 PHE cc_start: 0.7772 (t80) cc_final: 0.7515 (t80) outliers start: 34 outliers final: 29 residues processed: 181 average time/residue: 0.2872 time to fit residues: 77.1439 Evaluate side-chains 184 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 244 ARG Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 534 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 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 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR 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 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 155 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16361 Z= 0.150 Angle : 0.486 12.655 22130 Z= 0.252 Chirality : 0.038 0.184 2528 Planarity : 0.003 0.050 2804 Dihedral : 3.947 19.528 2153 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.94 % Allowed : 10.80 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1821 helix: 2.20 (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 TRP 0.007 0.001 TRP 5 777 HIS 0.003 0.001 HIS 5 474 PHE 0.019 0.001 PHE 1 515 TYR 0.010 0.001 TYR 1 103 ARG 0.005 0.000 ARG 5 893 *********************** 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 201 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.946 Fit side-chains REVERT: 5 244 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: 8 227 ILE cc_start: 0.8944 (mt) cc_final: 0.8567 (mp) REVERT: 4 284 ASN cc_start: 0.8226 (t0) cc_final: 0.7708 (t0) REVERT: 9 250 PHE cc_start: 0.7760 (t80) cc_final: 0.7404 (t80) outliers start: 31 outliers final: 23 residues processed: 190 average time/residue: 0.2937 time to fit residues: 83.8951 Evaluate side-chains 189 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 244 ARG 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 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 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 612 ILE Chi-restraints excluded: chain 1 residue 709 SER Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 225 SER Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 593 GLN 8 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16361 Z= 0.322 Angle : 0.580 12.585 22130 Z= 0.299 Chirality : 0.041 0.230 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.327 20.590 2153 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.70 % Allowed : 11.21 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1821 helix: 1.95 (0.16), residues: 1036 sheet: 0.72 (0.46), residues: 134 loop : -1.54 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 604 HIS 0.006 0.001 HIS 5 474 PHE 0.022 0.002 PHE 1 515 TYR 0.014 0.002 TYR 9 234 ARG 0.006 0.000 ARG 5 893 ********************** 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 181 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.996 Fit side-chains REVERT: 5 244 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7367 (ttm170) REVERT: 8 227 ILE cc_start: 0.8970 (mt) cc_final: 0.8617 (mp) REVERT: 4 284 ASN cc_start: 0.8279 (t0) cc_final: 0.7775 (t0) REVERT: 9 250 PHE cc_start: 0.7828 (t80) cc_final: 0.7483 (t80) outliers start: 27 outliers final: 25 residues processed: 171 average time/residue: 0.3058 time to fit residues: 77.3131 Evaluate side-chains 179 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 244 ARG Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 584 ASN 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 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 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 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 225 SER Chi-restraints excluded: chain 4 residue 272 ILE 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 167 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099962 restraints weight = 31682.631| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.50 r_work: 0.2674 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 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 = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16361 Z= 0.261 Angle : 0.547 13.339 22130 Z= 0.283 Chirality : 0.040 0.202 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.257 20.185 2153 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.70 % Allowed : 11.27 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1821 helix: 1.97 (0.16), residues: 1036 sheet: 0.68 (0.47), residues: 133 loop : -1.52 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 604 HIS 0.005 0.001 HIS 9 314 PHE 0.021 0.001 PHE 1 515 TYR 0.014 0.001 TYR 9 234 ARG 0.005 0.000 ARG 5 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.60 seconds wall clock time: 56 minutes 27.90 seconds (3387.90 seconds total)