Starting phenix.real_space_refine on Mon Feb 19 06:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/02_2024/8gjl_40093_updated.pdb" } resolution = 3.44 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 15512 2.51 5 N 3856 2.21 5 O 4463 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B GLU 956": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C ASP 807": "OD1" <-> "OD2" Residue "C GLU 839": "OE1" <-> "OE2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C GLU 941": "OE1" <-> "OE2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C GLU 956": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23916 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7932 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7978 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 8006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8006 Unusual residues: {'CPF': 1} Classifications: {'peptide': 1032, 'undetermined': 1} Link IDs: {'PTRANS': 41, 'TRANS': 990, None: 1} Not linked: pdbres="LYS C1032 " pdbres="CPF C1101 " Time building chain proxies: 13.00, per 1000 atoms: 0.54 Number of scatterers: 23916 At special positions: 0 Unit cell: (114.49, 123.05, 147.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 F 1 9.00 O 4463 8.00 N 3856 7.00 C 15512 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 - 3.50 Amino acid : False - 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: 10.12 Conformation dependent library (CDL) restraints added in 4.3 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 24 sheets defined 55.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.88 Creating SS restraints... Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.548A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.263A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.530A pdb=" N LYS B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.019A pdb=" N ASN B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 330 through 359 removed outlier: 4.390A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 387 Proline residue: B 369 - end of helix removed outlier: 3.595A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix removed outlier: 3.603A pdb=" N THR B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 423 removed outlier: 5.218A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 459 removed outlier: 5.267A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix Processing helix chain 'B' and resid 465 through 497 removed outlier: 4.405A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 536 through 555 Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.791A pdb=" N GLN B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 686 through 701 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 770 through 774 Processing helix chain 'B' and resid 776 through 781 removed outlier: 4.536A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 780 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 856 through 862 Processing helix chain 'B' and resid 868 through 886 Processing helix chain 'B' and resid 891 through 913 removed outlier: 3.796A pdb=" N THR B 897 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 899 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Proline residue: B 900 - end of helix Processing helix chain 'B' and resid 919 through 949 Processing helix chain 'B' and resid 954 through 984 removed outlier: 4.505A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix Processing helix chain 'B' and resid 991 through 1031 removed outlier: 3.677A pdb=" N GLY B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1014 " --> pdb=" O THR B1010 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.734A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.248A pdb=" N THR A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 100 through 117 removed outlier: 5.178A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 151 through 168 removed outlier: 4.267A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASP A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.777A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 363 through 387 Proline residue: A 369 - end of helix Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 393 through 423 removed outlier: 4.253A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 460 removed outlier: 5.174A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Proline residue: A 457 - end of helix removed outlier: 3.906A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 498 removed outlier: 3.620A pdb=" N ILE A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.652A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.673A pdb=" N GLN A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 removed outlier: 5.011A pdb=" N ALA A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 736 through 747 Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 778 through 781 No H-bonds generated for 'chain 'A' and resid 778 through 781' Processing helix chain 'A' and resid 830 through 844 Processing helix chain 'A' and resid 855 through 863 Processing helix chain 'A' and resid 866 through 886 Processing helix chain 'A' and resid 891 through 913 removed outlier: 3.791A pdb=" N ALA A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Proline residue: A 900 - end of helix Processing helix chain 'A' and resid 919 through 949 removed outlier: 4.070A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 985 removed outlier: 4.869A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix removed outlier: 3.570A pdb=" N PHE A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1031 removed outlier: 3.923A pdb=" N ALA A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.674A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 30 Processing helix chain 'C' and resid 55 through 70 removed outlier: 4.111A pdb=" N THR C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.727A pdb=" N ALA C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 300 through 316 removed outlier: 3.907A pdb=" N LYS C 316 " --> pdb=" O GLN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 360 removed outlier: 3.576A pdb=" N VAL C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 387 Proline residue: C 369 - end of helix removed outlier: 4.717A pdb=" N VAL C 373 " --> pdb=" O MET C 370 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 393 through 423 removed outlier: 4.145A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 460 removed outlier: 5.393A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix removed outlier: 3.566A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Proline residue: C 457 - end of helix removed outlier: 3.851A pdb=" N PHE C 460 " --> pdb=" O ILE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 497 removed outlier: 4.276A pdb=" N THR C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 555 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.753A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 686 through 702 removed outlier: 3.583A pdb=" N THR C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 770 through 773 No H-bonds generated for 'chain 'C' and resid 770 through 773' Processing helix chain 'C' and resid 778 through 781 No H-bonds generated for 'chain 'C' and resid 778 through 781' Processing helix chain 'C' and resid 830 through 844 Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 866 through 886 Processing helix chain 'C' and resid 891 through 913 Proline residue: C 900 - end of helix removed outlier: 3.938A pdb=" N VAL C 903 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 913 " --> pdb=" O VAL C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 948 Processing helix chain 'C' and resid 954 through 985 removed outlier: 4.507A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 3.787A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1031 removed outlier: 4.198A pdb=" N ALA C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.876A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.691A pdb=" N ILE B 292 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 139 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 290 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 141 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 288 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 267 through 273 removed outlier: 8.474A pdb=" N ASN B 761 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N MET B 185 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN B 763 " --> pdb=" O MET B 185 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE B 187 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B 765 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 189 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 767 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN B 753 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 766 " --> pdb=" O TYR B 751 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR B 751 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 279 through 282 removed outlier: 6.584A pdb=" N ILE B 627 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 604 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE B 625 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 606 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 623 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE B 608 " --> pdb=" O ALA B 621 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA B 621 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 850 through 854 removed outlier: 4.110A pdb=" N GLU B 675 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 717 through 724 Processing sheet with id= G, first strand: chain 'B' and resid 783 through 785 Processing sheet with id= H, first strand: chain 'B' and resid 251 through 254 removed outlier: 6.979A pdb=" N LEU B 261 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.432A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.957A pdb=" N ILE A 292 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 139 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 290 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 141 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 288 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 267 through 273 removed outlier: 7.985A pdb=" N TYR A 183 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 763 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 765 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 279 through 282 removed outlier: 6.653A pdb=" N ILE A 627 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 604 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 625 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A 606 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 623 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE A 608 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA A 621 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 817 through 822 removed outlier: 3.685A pdb=" N ALA A 818 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 675 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 854 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 718 through 724 Processing sheet with id= O, first strand: chain 'A' and resid 783 through 785 Processing sheet with id= P, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.654A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 322 through 326 removed outlier: 6.708A pdb=" N ILE C 292 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 139 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE C 290 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C 141 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 288 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 267 through 273 removed outlier: 7.630A pdb=" N TYR C 183 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN C 763 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C 765 " --> pdb=" O MET C 185 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 655 through 661 Processing sheet with id= T, first strand: chain 'C' and resid 817 through 822 removed outlier: 3.584A pdb=" N ALA C 818 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 822 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 675 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 718 through 724 Processing sheet with id= V, first strand: chain 'C' and resid 783 through 785 Processing sheet with id= W, first strand: chain 'C' and resid 251 through 254 removed outlier: 7.095A pdb=" N LEU C 261 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 601 through 604 removed outlier: 6.847A pdb=" N ILE C 627 " --> pdb=" O SER C 602 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 3960 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: 9.05 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3941 1.32 - 1.44: 6191 1.44 - 1.57: 14084 1.57 - 1.69: 1 1.69 - 1.82: 162 Bond restraints: 24379 Sorted by residual: bond pdb=" C10 CPF C1101 " pdb=" C5 CPF C1101 " ideal model delta sigma weight residual 1.399 1.483 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C VAL A 407 " pdb=" O VAL A 407 " ideal model delta sigma weight residual 1.238 1.191 0.047 1.18e-02 7.18e+03 1.58e+01 bond pdb=" C7 CPF C1101 " pdb=" C8 CPF C1101 " ideal model delta sigma weight residual 1.410 1.483 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C CYS A 452 " pdb=" O CYS A 452 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.22e-02 6.72e+03 8.90e+00 bond pdb=" C SER A 973 " pdb=" O SER A 973 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.16e-02 7.43e+03 8.47e+00 ... (remaining 24374 not shown) Histogram of bond angle deviations from ideal: 59.89 - 74.73: 3 74.73 - 89.57: 0 89.57 - 104.41: 342 104.41 - 119.25: 20049 119.25 - 134.09: 12731 Bond angle restraints: 33125 Sorted by residual: angle pdb=" CB PRO B 562 " pdb=" CG PRO B 562 " pdb=" CD PRO B 562 " ideal model delta sigma weight residual 106.10 89.90 16.20 3.20e+00 9.77e-02 2.56e+01 angle pdb=" N ILE A 929 " pdb=" CA ILE A 929 " pdb=" C ILE A 929 " ideal model delta sigma weight residual 110.42 105.70 4.72 9.60e-01 1.09e+00 2.42e+01 angle pdb=" N LEU C 137 " pdb=" CA LEU C 137 " pdb=" C LEU C 137 " ideal model delta sigma weight residual 113.88 107.86 6.02 1.23e+00 6.61e-01 2.40e+01 angle pdb=" N LEU A 928 " pdb=" CA LEU A 928 " pdb=" C LEU A 928 " ideal model delta sigma weight residual 112.23 106.07 6.16 1.26e+00 6.30e-01 2.39e+01 angle pdb=" C ILE A 939 " pdb=" CA ILE A 939 " pdb=" CB ILE A 939 " ideal model delta sigma weight residual 112.24 105.99 6.25 1.34e+00 5.57e-01 2.17e+01 ... (remaining 33120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 13733 23.61 - 47.23: 847 47.23 - 70.84: 70 70.84 - 94.46: 12 94.46 - 118.07: 1 Dihedral angle restraints: 14663 sinusoidal: 5625 harmonic: 9038 Sorted by residual: dihedral pdb=" CA PHE B 976 " pdb=" C PHE B 976 " pdb=" N THR B 977 " pdb=" CA THR B 977 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C15 CPF C1101 " pdb=" C16 CPF C1101 " pdb=" N3 CPF C1101 " pdb=" C17 CPF C1101 " ideal model delta sinusoidal sigma weight residual -60.38 57.69 -118.07 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CA TYR B 828 " pdb=" C TYR B 828 " pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3438 0.063 - 0.126: 455 0.126 - 0.188: 40 0.188 - 0.251: 7 0.251 - 0.314: 2 Chirality restraints: 3942 Sorted by residual: chirality pdb=" CA ILE A 929 " pdb=" N ILE A 929 " pdb=" C ILE A 929 " pdb=" CB ILE A 929 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 CPF C1101 " pdb=" C12 CPF C1101 " pdb=" C13 CPF C1101 " pdb=" N1 CPF C1101 " both_signs ideal model delta sigma weight residual True 2.29 2.60 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU C 938 " pdb=" N LEU C 938 " pdb=" C LEU C 938 " pdb=" CB LEU C 938 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3939 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 118 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 119 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 288 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.08e+00 pdb=" N PRO C 289 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 289 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 289 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 901 " -0.017 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" CG PHE C 901 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 901 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 901 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 901 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 901 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 901 " 0.003 2.00e-02 2.50e+03 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 265 2.64 - 3.21: 24188 3.21 - 3.77: 37865 3.77 - 4.34: 52245 4.34 - 4.90: 86371 Nonbonded interactions: 200934 Sorted by model distance: nonbonded pdb=" OD1 ASP A 611 " pdb=" OG1 THR A 614 " model vdw 2.075 2.440 nonbonded pdb=" OE1 GLN A 312 " pdb=" OH TYR A 324 " model vdw 2.109 2.440 nonbonded pdb=" OG1 THR A 43 " pdb=" O VAL A 92 " model vdw 2.121 2.440 nonbonded pdb=" OG SER B 132 " pdb=" OD1 ASP B 174 " model vdw 2.127 2.440 nonbonded pdb=" O ASN C 212 " pdb=" ND2 ASN C 753 " model vdw 2.159 2.520 ... (remaining 200929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 through 221 or (resid 222 and (na \ me N or name CA or name C or name O or name CB )) or resid 223 through 255 or (r \ esid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 t \ hrough 418 or (resid 419 and (name N or name CA or name C or name O or name CB ) \ ) or resid 420 through 507 or (resid 508 and (name N or name CA or name C or nam \ e O or name CB )) or resid 509 through 536 or (resid 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throu \ gh 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or \ resid 704 through 1032)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 through 221 or (resid 222 and (na \ me N or name CA or name C or name O or name CB )) or resid 223 through 255 or (r \ esid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 t \ hrough 418 or (resid 419 and (name N or name CA or name C or name O or name CB ) \ ) or resid 420 through 507 or (resid 508 and (name N or name CA or name C or nam \ e O or name CB )) or resid 509 through 536 or (resid 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throu \ gh 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or \ resid 704 through 1031 or (resid 1032 and (name N or name CA or name C or name \ O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 10.390 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 65.700 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.118 24379 Z= 0.256 Angle : 0.692 16.199 33125 Z= 0.394 Chirality : 0.044 0.314 3942 Planarity : 0.005 0.077 4197 Dihedral : 14.151 118.073 8819 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.65 % Allowed : 15.53 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.44 (0.15), residues: 3090 helix: 1.93 (0.12), residues: 1713 sheet: -0.04 (0.24), residues: 437 loop : -0.29 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 889 HIS 0.003 0.001 HIS B 995 PHE 0.042 0.001 PHE C 901 TYR 0.022 0.001 TYR B 530 ARG 0.012 0.001 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 495 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 430 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: B 540 LEU cc_start: 0.8799 (mm) cc_final: 0.8580 (mm) REVERT: B 676 MET cc_start: 0.8783 (tmm) cc_final: 0.8105 (tmm) REVERT: B 904 PHE cc_start: 0.8272 (t80) cc_final: 0.8068 (t80) REVERT: B 908 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9126 (pp) REVERT: B 913 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7761 (mmm-85) REVERT: B 965 ARG cc_start: 0.8798 (mmm160) cc_final: 0.7887 (mmm160) REVERT: A 22 ILE cc_start: 0.9612 (mp) cc_final: 0.9388 (mp) REVERT: A 381 PHE cc_start: 0.8910 (m-80) cc_final: 0.8665 (m-80) REVERT: A 928 LEU cc_start: 0.8874 (mt) cc_final: 0.8661 (mt) REVERT: C 109 ASN cc_start: 0.8124 (m-40) cc_final: 0.7753 (m-40) REVERT: C 185 MET cc_start: 0.9002 (tpp) cc_final: 0.8623 (tpp) REVERT: C 415 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7815 (tt0) REVERT: C 438 ASN cc_start: 0.8070 (m-40) cc_final: 0.7862 (m-40) outliers start: 17 outliers final: 5 residues processed: 502 average time/residue: 0.3038 time to fit residues: 251.1419 Evaluate side-chains 422 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 415 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 302 ASN B 690 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN C 514 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24379 Z= 0.213 Angle : 0.605 8.503 33125 Z= 0.307 Chirality : 0.043 0.283 3942 Planarity : 0.005 0.050 4197 Dihedral : 5.240 88.126 3327 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.86 % Allowed : 16.53 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.39 (0.15), residues: 3090 helix: 1.85 (0.12), residues: 1709 sheet: -0.04 (0.24), residues: 443 loop : -0.24 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 853 HIS 0.006 0.001 HIS B 422 PHE 0.025 0.001 PHE C 610 TYR 0.026 0.002 TYR B 849 ARG 0.005 0.000 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 472 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8924 (m-10) cc_final: 0.8653 (m-10) REVERT: B 470 ARG cc_start: 0.8989 (ttt180) cc_final: 0.8347 (ttm110) REVERT: B 540 LEU cc_start: 0.8727 (mm) cc_final: 0.8495 (mm) REVERT: B 676 MET cc_start: 0.8682 (tmm) cc_final: 0.8220 (tmm) REVERT: B 904 PHE cc_start: 0.8663 (t80) cc_final: 0.8409 (t80) REVERT: A 381 PHE cc_start: 0.8893 (m-80) cc_final: 0.8583 (m-80) REVERT: C 109 ASN cc_start: 0.8197 (m-40) cc_final: 0.7749 (m-40) REVERT: C 415 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 438 ASN cc_start: 0.8076 (m-40) cc_final: 0.7859 (m-40) outliers start: 75 outliers final: 45 residues processed: 510 average time/residue: 0.3133 time to fit residues: 269.5555 Evaluate side-chains 465 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 420 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 903 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 0.0270 chunk 281 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 250 optimal weight: 0.0470 chunk 278 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN A 102 GLN A 295 GLN A 299 ASN A 594 ASN A 776 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 922 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24379 Z= 0.282 Angle : 0.603 10.313 33125 Z= 0.307 Chirality : 0.043 0.248 3942 Planarity : 0.004 0.049 4197 Dihedral : 4.466 50.238 3320 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.51 % Allowed : 17.60 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.29 (0.15), residues: 3090 helix: 1.78 (0.12), residues: 1712 sheet: -0.17 (0.23), residues: 458 loop : -0.23 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.028 0.002 PHE B 455 TYR 0.025 0.002 TYR C 508 ARG 0.003 0.000 ARG C 965 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 456 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8932 (m-10) cc_final: 0.8604 (m-10) REVERT: B 430 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8928 (tttt) REVERT: B 540 LEU cc_start: 0.8730 (mm) cc_final: 0.8500 (mm) REVERT: B 676 MET cc_start: 0.8655 (tmm) cc_final: 0.8154 (tmm) REVERT: B 904 PHE cc_start: 0.8722 (t80) cc_final: 0.8519 (t80) REVERT: B 916 ASP cc_start: 0.7956 (m-30) cc_final: 0.7444 (t70) REVERT: A 381 PHE cc_start: 0.8854 (m-80) cc_final: 0.8468 (m-80) REVERT: A 873 LEU cc_start: 0.8552 (tp) cc_final: 0.8351 (tp) REVERT: A 925 LEU cc_start: 0.9457 (tt) cc_final: 0.9255 (tt) REVERT: A 928 LEU cc_start: 0.8795 (mt) cc_final: 0.8544 (mt) REVERT: A 981 LEU cc_start: 0.8930 (mt) cc_final: 0.8683 (mt) REVERT: C 415 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7821 (tt0) REVERT: C 438 ASN cc_start: 0.8066 (m-40) cc_final: 0.7852 (m-40) REVERT: C 717 PHE cc_start: 0.8438 (m-80) cc_final: 0.8227 (m-80) REVERT: C 934 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8207 (ttpt) outliers start: 92 outliers final: 62 residues processed: 514 average time/residue: 0.2929 time to fit residues: 251.7146 Evaluate side-chains 483 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 420 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 983 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 80 optimal weight: 0.0020 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 392 ASN A 594 ASN C 102 GLN C 109 ASN C 180 ASN C 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24379 Z= 0.189 Angle : 0.582 11.024 33125 Z= 0.293 Chirality : 0.042 0.302 3942 Planarity : 0.004 0.051 4197 Dihedral : 4.412 55.207 3320 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.05 % Allowed : 19.12 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.29 (0.15), residues: 3090 helix: 1.75 (0.12), residues: 1711 sheet: -0.11 (0.23), residues: 452 loop : -0.23 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 853 HIS 0.004 0.001 HIS B 422 PHE 0.022 0.001 PHE A 345 TYR 0.027 0.001 TYR B 849 ARG 0.003 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 465 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8516 (tmm) cc_final: 0.8308 (tmm) REVERT: B 397 PHE cc_start: 0.8919 (m-10) cc_final: 0.8660 (m-10) REVERT: B 417 ILE cc_start: 0.9522 (mt) cc_final: 0.9163 (tp) REVERT: B 430 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8973 (tttt) REVERT: B 540 LEU cc_start: 0.8735 (mm) cc_final: 0.8497 (mm) REVERT: B 676 MET cc_start: 0.8610 (tmm) cc_final: 0.8189 (tmm) REVERT: B 701 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8577 (ttm-80) REVERT: B 976 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8278 (t80) REVERT: A 381 PHE cc_start: 0.8875 (m-80) cc_final: 0.8494 (m-80) REVERT: A 469 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: A 873 LEU cc_start: 0.8454 (tp) cc_final: 0.8204 (tp) REVERT: A 981 LEU cc_start: 0.8906 (mt) cc_final: 0.8670 (mt) REVERT: C 180 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6706 (t0) REVERT: C 408 ASP cc_start: 0.7972 (t0) cc_final: 0.7555 (t0) REVERT: C 934 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8060 (ttpt) outliers start: 80 outliers final: 52 residues processed: 513 average time/residue: 0.3011 time to fit residues: 259.0386 Evaluate side-chains 490 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 434 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 983 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 594 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24379 Z= 0.260 Angle : 0.609 11.044 33125 Z= 0.307 Chirality : 0.043 0.298 3942 Planarity : 0.004 0.048 4197 Dihedral : 4.428 59.682 3318 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.24 % Allowed : 21.11 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.22 (0.15), residues: 3090 helix: 1.72 (0.13), residues: 1711 sheet: -0.17 (0.23), residues: 458 loop : -0.28 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.025 0.001 PHE C 717 TYR 0.020 0.001 TYR B 849 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 443 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ASN cc_start: 0.8489 (m-40) cc_final: 0.8178 (m-40) REVERT: B 397 PHE cc_start: 0.8932 (m-10) cc_final: 0.8692 (m-10) REVERT: B 430 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (tttt) REVERT: B 540 LEU cc_start: 0.8740 (mm) cc_final: 0.8496 (mm) REVERT: B 676 MET cc_start: 0.8595 (tmm) cc_final: 0.8203 (tmm) REVERT: B 701 ARG cc_start: 0.8790 (ttm110) cc_final: 0.8579 (ttm-80) REVERT: B 877 PHE cc_start: 0.9160 (m-10) cc_final: 0.8886 (m-10) REVERT: B 976 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (t80) REVERT: A 381 PHE cc_start: 0.8879 (m-80) cc_final: 0.8446 (m-80) REVERT: A 469 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: A 873 LEU cc_start: 0.8516 (tp) cc_final: 0.8257 (tp) REVERT: A 981 LEU cc_start: 0.8917 (mt) cc_final: 0.8678 (mt) REVERT: C 408 ASP cc_start: 0.7938 (t0) cc_final: 0.7496 (t0) REVERT: C 568 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9240 (m) REVERT: C 934 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8008 (ttpt) outliers start: 85 outliers final: 68 residues processed: 497 average time/residue: 0.2983 time to fit residues: 247.3778 Evaluate side-chains 502 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 430 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 983 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24379 Z= 0.221 Angle : 0.606 14.041 33125 Z= 0.302 Chirality : 0.043 0.336 3942 Planarity : 0.004 0.049 4197 Dihedral : 4.369 55.440 3318 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.05 % Allowed : 21.98 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.23 (0.15), residues: 3090 helix: 1.70 (0.13), residues: 1711 sheet: -0.07 (0.23), residues: 462 loop : -0.29 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.025 0.001 PHE C 717 TYR 0.021 0.001 TYR B 530 ARG 0.004 0.000 ARG C 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 449 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8904 (m-10) cc_final: 0.8657 (m-10) REVERT: B 430 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8991 (tttt) REVERT: B 676 MET cc_start: 0.8618 (tmm) cc_final: 0.8212 (tmm) REVERT: B 701 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8542 (ttm-80) REVERT: B 877 PHE cc_start: 0.9192 (m-10) cc_final: 0.8902 (m-10) REVERT: B 978 PHE cc_start: 0.8199 (m-80) cc_final: 0.7901 (m-10) REVERT: A 381 PHE cc_start: 0.8849 (m-80) cc_final: 0.8391 (m-80) REVERT: A 469 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: A 873 LEU cc_start: 0.8527 (tp) cc_final: 0.8255 (tp) REVERT: A 981 LEU cc_start: 0.8909 (mt) cc_final: 0.8658 (mt) REVERT: C 185 MET cc_start: 0.9168 (tpp) cc_final: 0.8840 (tpt) REVERT: C 408 ASP cc_start: 0.7941 (t0) cc_final: 0.7431 (t0) REVERT: C 568 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9230 (m) REVERT: C 934 LYS cc_start: 0.8570 (ttpt) cc_final: 0.7869 (ttpt) outliers start: 80 outliers final: 63 residues processed: 499 average time/residue: 0.3048 time to fit residues: 253.3598 Evaluate side-chains 493 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 427 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 983 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 169 optimal weight: 0.0970 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 181 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 275 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24379 Z= 0.219 Angle : 0.614 12.238 33125 Z= 0.306 Chirality : 0.044 0.325 3942 Planarity : 0.004 0.049 4197 Dihedral : 4.257 35.936 3316 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.09 % Allowed : 22.33 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.22 (0.15), residues: 3090 helix: 1.67 (0.13), residues: 1708 sheet: 0.05 (0.23), residues: 442 loop : -0.30 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.036 0.001 PHE B 976 TYR 0.021 0.001 TYR B 530 ARG 0.003 0.000 ARG C 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 441 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8895 (m-10) cc_final: 0.8653 (m-10) REVERT: B 430 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8995 (tttt) REVERT: B 676 MET cc_start: 0.8624 (tmm) cc_final: 0.8210 (tmm) REVERT: B 701 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8528 (ttm-80) REVERT: B 729 MET cc_start: 0.8947 (ttp) cc_final: 0.8742 (ttp) REVERT: B 877 PHE cc_start: 0.9229 (m-10) cc_final: 0.8936 (m-10) REVERT: A 381 PHE cc_start: 0.8807 (m-80) cc_final: 0.8310 (m-80) REVERT: A 469 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8462 (mp10) REVERT: A 873 LEU cc_start: 0.8535 (tp) cc_final: 0.8255 (tp) REVERT: A 971 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: C 185 MET cc_start: 0.9167 (tpp) cc_final: 0.8838 (tpt) REVERT: C 568 VAL cc_start: 0.9445 (OUTLIER) cc_final: 0.9228 (m) REVERT: C 934 LYS cc_start: 0.8596 (ttpt) cc_final: 0.7994 (ttpt) REVERT: C 1005 MET cc_start: 0.8267 (mmm) cc_final: 0.8056 (mmm) outliers start: 81 outliers final: 61 residues processed: 493 average time/residue: 0.3074 time to fit residues: 253.0281 Evaluate side-chains 493 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 428 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 952 LYS Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN C 102 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 24379 Z= 0.246 Angle : 0.627 11.165 33125 Z= 0.314 Chirality : 0.044 0.334 3942 Planarity : 0.004 0.050 4197 Dihedral : 4.255 36.001 3316 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.13 % Allowed : 22.94 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.18 (0.15), residues: 3090 helix: 1.66 (0.13), residues: 1705 sheet: -0.06 (0.23), residues: 455 loop : -0.33 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 853 HIS 0.004 0.001 HIS B 995 PHE 0.026 0.001 PHE B 976 TYR 0.021 0.001 TYR A 677 ARG 0.005 0.000 ARG C 965 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 441 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ASN cc_start: 0.8616 (m-40) cc_final: 0.8266 (m-40) REVERT: B 397 PHE cc_start: 0.8859 (m-10) cc_final: 0.8629 (m-10) REVERT: B 430 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8778 (tttm) REVERT: B 676 MET cc_start: 0.8643 (tmm) cc_final: 0.8209 (tmm) REVERT: B 701 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8465 (ttm-80) REVERT: B 877 PHE cc_start: 0.9249 (m-10) cc_final: 0.8953 (m-10) REVERT: B 916 ASP cc_start: 0.8387 (p0) cc_final: 0.7821 (t0) REVERT: B 978 PHE cc_start: 0.8270 (m-10) cc_final: 0.8004 (m-80) REVERT: A 381 PHE cc_start: 0.8853 (m-80) cc_final: 0.8376 (m-80) REVERT: A 469 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: A 545 MET cc_start: 0.8635 (ttp) cc_final: 0.8384 (tmm) REVERT: A 873 LEU cc_start: 0.8557 (tp) cc_final: 0.8272 (tp) REVERT: C 185 MET cc_start: 0.9150 (tpp) cc_final: 0.8836 (tpt) REVERT: C 568 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9235 (m) REVERT: C 676 MET cc_start: 0.8527 (tpt) cc_final: 0.8240 (tpt) outliers start: 82 outliers final: 65 residues processed: 492 average time/residue: 0.3016 time to fit residues: 247.3844 Evaluate side-chains 494 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 426 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 952 LYS Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 3.9990 chunk 285 optimal weight: 0.2980 chunk 260 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 0.0030 chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 24379 Z= 0.204 Angle : 0.631 10.735 33125 Z= 0.315 Chirality : 0.044 0.381 3942 Planarity : 0.004 0.051 4197 Dihedral : 4.230 35.657 3316 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.75 % Allowed : 23.70 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.17 (0.15), residues: 3090 helix: 1.64 (0.13), residues: 1704 sheet: 0.00 (0.23), residues: 448 loop : -0.31 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.027 0.001 PHE A 345 TYR 0.020 0.001 TYR B 530 ARG 0.009 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 440 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8839 (m-10) cc_final: 0.8613 (m-10) REVERT: B 430 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8768 (tttm) REVERT: B 676 MET cc_start: 0.8621 (tmm) cc_final: 0.8199 (tmm) REVERT: B 701 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8476 (ttm-80) REVERT: B 877 PHE cc_start: 0.9313 (m-10) cc_final: 0.9015 (m-10) REVERT: B 916 ASP cc_start: 0.8344 (p0) cc_final: 0.7800 (t70) REVERT: B 978 PHE cc_start: 0.8326 (m-10) cc_final: 0.8099 (m-80) REVERT: A 381 PHE cc_start: 0.8826 (m-80) cc_final: 0.8367 (m-80) REVERT: A 469 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: A 873 LEU cc_start: 0.8517 (tp) cc_final: 0.8239 (tp) REVERT: C 185 MET cc_start: 0.9167 (tpp) cc_final: 0.8827 (tpt) REVERT: C 568 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9221 (m) REVERT: C 676 MET cc_start: 0.8527 (tpt) cc_final: 0.8235 (tpt) outliers start: 72 outliers final: 56 residues processed: 482 average time/residue: 0.3073 time to fit residues: 247.0396 Evaluate side-chains 483 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 424 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 952 LYS Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 204 optimal weight: 0.0670 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 238 GLN C 109 ASN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 24379 Z= 0.196 Angle : 0.637 14.583 33125 Z= 0.317 Chirality : 0.044 0.387 3942 Planarity : 0.004 0.052 4197 Dihedral : 4.190 35.483 3316 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.14 % Allowed : 24.89 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.15 (0.15), residues: 3090 helix: 1.59 (0.13), residues: 1707 sheet: 0.07 (0.24), residues: 436 loop : -0.31 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 519 HIS 0.003 0.001 HIS B 995 PHE 0.026 0.001 PHE A 921 TYR 0.020 0.001 TYR B 530 ARG 0.006 0.000 ARG A 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 439 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8830 (m-10) cc_final: 0.8610 (m-10) REVERT: B 430 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8762 (tttm) REVERT: B 676 MET cc_start: 0.8608 (tmm) cc_final: 0.8204 (tmm) REVERT: B 877 PHE cc_start: 0.9325 (m-10) cc_final: 0.9032 (m-10) REVERT: B 978 PHE cc_start: 0.8261 (m-10) cc_final: 0.8007 (m-80) REVERT: A 381 PHE cc_start: 0.8804 (m-80) cc_final: 0.8311 (m-80) REVERT: A 469 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: A 873 LEU cc_start: 0.8507 (tp) cc_final: 0.8233 (tp) REVERT: C 185 MET cc_start: 0.9173 (tpp) cc_final: 0.8629 (tpp) REVERT: C 568 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9220 (m) REVERT: C 676 MET cc_start: 0.8533 (tpt) cc_final: 0.7509 (tpt) outliers start: 56 outliers final: 49 residues processed: 472 average time/residue: 0.3175 time to fit residues: 250.2678 Evaluate side-chains 478 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 426 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 952 LYS Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 226 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 245 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087292 restraints weight = 58577.427| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.16 r_work: 0.3248 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 24379 Z= 0.210 Angle : 0.651 13.509 33125 Z= 0.322 Chirality : 0.044 0.399 3942 Planarity : 0.004 0.051 4197 Dihedral : 4.170 35.365 3316 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.10 % Allowed : 25.53 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.14 (0.15), residues: 3090 helix: 1.58 (0.13), residues: 1705 sheet: 0.09 (0.24), residues: 436 loop : -0.31 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 853 HIS 0.003 0.001 HIS B 995 PHE 0.029 0.001 PHE A 345 TYR 0.021 0.001 TYR C 385 ARG 0.012 0.000 ARG B 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.10 seconds wall clock time: 106 minutes 10.29 seconds (6370.29 seconds total)