Starting phenix.real_space_refine on Sun Apr 7 02:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/04_2024/7bsv_30168_trim_updated.pdb" } resolution = 3.0 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= 0.004 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 C 6081 2.51 5 N 1504 2.21 5 O 1702 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.58, per 1000 atoms: 0.60 Number of scatterers: 9339 At special positions: 0 Unit cell: (101.26, 93.79, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1702 8.00 N 1504 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-4 " NAG B 1 " - " MAN B 2 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 402 " - " ASN C 294 " " NAG C 403 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 40.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.578A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.574A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 120 removed outlier: 3.899A pdb=" N GLY A 92 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 3.713A pdb=" N VAL A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 100 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 101 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 103 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 105 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 109 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 118 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 283 through 313 removed outlier: 3.503A pdb=" N ASN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.550A pdb=" N MET A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 376 removed outlier: 3.510A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.956A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.600A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.785A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 719 removed outlier: 3.502A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.910A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.715A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 removed outlier: 3.519A pdb=" N ARG A 800 " --> pdb=" O ALA A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 No H-bonds generated for 'chain 'A' and resid 821 through 824' Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.675A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 853 through 859 removed outlier: 4.040A pdb=" N LYS A 857 " --> pdb=" O HIS A 854 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 893 removed outlier: 3.621A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.109A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 932 through 935 No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 939 through 945 removed outlier: 3.536A pdb=" N LYS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 977 removed outlier: 3.597A pdb=" N THR A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1014 removed outlier: 3.692A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 3.548A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 3.559A pdb=" N LEU A1061 " --> pdb=" O PHE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1076 removed outlier: 3.641A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1087 removed outlier: 3.573A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'C' and resid 53 through 73 removed outlier: 3.641A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.555A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.796A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.783A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 323 through 346 removed outlier: 3.538A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 124 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.803A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.955A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.530A pdb=" N LEU A 239 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 225 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 829 through 832 removed outlier: 6.346A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 785 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASP A 752 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.029A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 106 through 110 removed outlier: 3.514A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1465 1.30 - 1.43: 2578 1.43 - 1.56: 5449 1.56 - 1.68: 1 1.68 - 1.81: 71 Bond restraints: 9564 Sorted by residual: bond pdb=" C17 P5S A1103 " pdb=" O19 P5S A1103 " ideal model delta sigma weight residual 1.328 1.453 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.796 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.796 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.93e+01 ... (remaining 9559 not shown) Histogram of bond angle deviations from ideal: 89.52 - 107.55: 363 107.55 - 125.59: 12452 125.59 - 143.62: 151 143.62 - 161.66: 0 161.66 - 179.69: 2 Bond angle restraints: 12968 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.69 -71.01 3.00e+00 1.11e-01 5.60e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.28 -69.65 3.00e+00 1.11e-01 5.39e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.09 20.12 3.00e+00 1.11e-01 4.50e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.52 20.07 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 90.20 19.49 3.00e+00 1.11e-01 4.22e+01 ... (remaining 12963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 5242 24.83 - 49.65: 390 49.65 - 74.48: 69 74.48 - 99.31: 21 99.31 - 124.13: 10 Dihedral angle restraints: 5732 sinusoidal: 2387 harmonic: 3345 Sorted by residual: dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 180.00 121.36 58.64 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 153.74 -60.74 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CA VAL C 99 " pdb=" C VAL C 99 " pdb=" N THR C 100 " pdb=" CA THR C 100 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 5729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1461 0.148 - 0.295: 1 0.295 - 0.443: 0 0.443 - 0.591: 1 0.591 - 0.738: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C1 MAN B 2 " pdb=" O4 NAG B 1 " pdb=" C2 MAN B 2 " pdb=" O5 MAN B 2 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 6.00e+02 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 107 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1462 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C 403 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 107 " 0.124 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" CG ASN C 107 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 107 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 107 " -0.417 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " 0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.068 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C7 NAG C 401 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.056 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 64 2.43 - 3.05: 6138 3.05 - 3.66: 13271 3.66 - 4.28: 23144 4.28 - 4.90: 37510 Nonbonded interactions: 80127 Sorted by model distance: nonbonded pdb=" F4 ALF A1101 " pdb="MG MG A1102 " model vdw 1.809 2.120 nonbonded pdb=" OG1 THR A 175 " pdb=" OD2 ASP A 179 " model vdw 2.042 2.440 nonbonded pdb=" O GLY C 84 " pdb=" OG1 THR C 85 " model vdw 2.054 2.440 nonbonded pdb=" O TYR A 188 " pdb=" ND2 ASN A 243 " model vdw 2.079 2.520 nonbonded pdb=" ND2 ASN C 216 " pdb=" O GLY C 251 " model vdw 2.101 2.520 ... (remaining 80122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.010 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: 4.060 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.005 0.125 9564 Z= 0.347 Angle : 1.149 71.014 12968 Z= 0.459 Chirality : 0.050 0.738 1465 Planarity : 0.008 0.292 1612 Dihedral : 18.881 124.132 3565 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.21 % Rotamer: Outliers : 6.19 % Allowed : 22.12 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -6.02 (0.17), residues: 1129 helix: -4.44 (0.12), residues: 497 sheet: -2.74 (0.37), residues: 166 loop : -3.76 (0.21), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.014 0.001 PHE A 894 TYR 0.011 0.001 TYR A 324 ARG 0.002 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7524 (ptt180) REVERT: A 191 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7011 (mmp-170) REVERT: A 256 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8614 (pttp) REVERT: A 329 GLN cc_start: 0.8014 (tp40) cc_final: 0.7624 (mm-40) REVERT: A 676 ASP cc_start: 0.7872 (t0) cc_final: 0.7440 (t0) REVERT: A 703 LYS cc_start: 0.7720 (mtpm) cc_final: 0.6858 (mtmm) REVERT: A 774 ILE cc_start: 0.8693 (mt) cc_final: 0.8480 (mt) REVERT: A 926 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 27 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5779 (tpp80) REVERT: C 343 LEU cc_start: 0.8246 (pp) cc_final: 0.7948 (pt) outliers start: 63 outliers final: 21 residues processed: 195 average time/residue: 1.1768 time to fit residues: 246.6606 Evaluate side-chains 142 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 106 GLN A 121 ASN A 226 ASN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 392 ASN A 397 ASN A 764 GLN A 777 GLN A 819 ASN A 862 HIS C 36 GLN C 129 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 298 ASN C 347 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9564 Z= 0.183 Angle : 0.869 30.483 12968 Z= 0.380 Chirality : 0.045 0.461 1465 Planarity : 0.005 0.057 1612 Dihedral : 12.242 96.039 1417 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.60 % Allowed : 21.83 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -4.00 (0.21), residues: 1129 helix: -2.59 (0.18), residues: 504 sheet: -1.79 (0.39), residues: 164 loop : -2.90 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.005 0.001 HIS A 114 PHE 0.014 0.001 PHE A 894 TYR 0.016 0.001 TYR A 324 ARG 0.003 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7776 (ptm-80) cc_final: 0.7379 (tmt-80) REVERT: A 191 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7119 (mmp-170) REVERT: A 224 ARG cc_start: 0.7206 (ttm170) cc_final: 0.7003 (ttt90) REVERT: A 329 GLN cc_start: 0.8005 (tp40) cc_final: 0.7719 (mm-40) REVERT: A 364 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 385 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7959 (pt) REVERT: A 676 ASP cc_start: 0.7751 (t0) cc_final: 0.7453 (t0) REVERT: A 703 LYS cc_start: 0.7723 (mtpm) cc_final: 0.6827 (mtmm) REVERT: A 717 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: A 746 GLU cc_start: 0.5272 (OUTLIER) cc_final: 0.4951 (tt0) REVERT: A 926 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 928 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: A 1003 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8328 (tp) outliers start: 57 outliers final: 15 residues processed: 177 average time/residue: 1.1944 time to fit residues: 227.8963 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 226 ASN A 386 ASN A 777 GLN A 840 GLN A 872 HIS ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9564 Z= 0.309 Angle : 0.876 31.698 12968 Z= 0.385 Chirality : 0.047 0.308 1465 Planarity : 0.005 0.074 1612 Dihedral : 10.558 87.993 1388 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 5.80 % Allowed : 23.01 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -3.00 (0.23), residues: 1129 helix: -1.60 (0.21), residues: 504 sheet: -1.17 (0.41), residues: 166 loop : -2.65 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 236 HIS 0.005 0.001 HIS A 929 PHE 0.017 0.002 PHE C 108 TYR 0.015 0.002 TYR A 311 ARG 0.004 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 1.104 Fit side-chains REVERT: A 135 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7555 (ptt180) REVERT: A 191 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7184 (mmp-170) REVERT: A 385 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8011 (pt) REVERT: A 703 LYS cc_start: 0.7752 (mtpm) cc_final: 0.6832 (mtmm) REVERT: A 717 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: A 774 ILE cc_start: 0.8486 (mt) cc_final: 0.8174 (mp) REVERT: A 926 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 928 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: C 184 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6248 (pm20) outliers start: 59 outliers final: 29 residues processed: 165 average time/residue: 1.0730 time to fit residues: 191.5300 Evaluate side-chains 143 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 386 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9564 Z= 0.170 Angle : 0.822 29.847 12968 Z= 0.350 Chirality : 0.043 0.293 1465 Planarity : 0.004 0.070 1612 Dihedral : 9.664 89.055 1387 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.11 % Allowed : 23.80 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.18 % 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: -2.17 (0.24), residues: 1129 helix: -0.77 (0.22), residues: 504 sheet: -0.65 (0.43), residues: 159 loop : -2.44 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE A 894 TYR 0.015 0.001 TYR A 324 ARG 0.004 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.043 Fit side-chains REVERT: A 44 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7313 (ttt90) REVERT: A 135 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7393 (tmt-80) REVERT: A 191 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7029 (mmp-170) REVERT: A 385 ILE cc_start: 0.8178 (pt) cc_final: 0.7932 (pt) REVERT: A 717 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: A 774 ILE cc_start: 0.8480 (mt) cc_final: 0.8149 (mp) REVERT: A 926 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 928 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: C 155 LYS cc_start: 0.8193 (mttp) cc_final: 0.7865 (pttm) REVERT: C 238 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7791 (pttp) outliers start: 52 outliers final: 24 residues processed: 168 average time/residue: 1.0550 time to fit residues: 192.3097 Evaluate side-chains 139 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A1022 ASN C 36 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 9564 Z= 0.546 Angle : 0.939 34.713 12968 Z= 0.422 Chirality : 0.052 0.290 1465 Planarity : 0.005 0.070 1612 Dihedral : 9.817 88.474 1387 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 5.90 % Allowed : 23.01 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.18 % 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: -2.49 (0.23), residues: 1129 helix: -1.16 (0.22), residues: 502 sheet: -0.69 (0.42), residues: 167 loop : -2.51 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 236 HIS 0.007 0.002 HIS A 929 PHE 0.019 0.002 PHE A 884 TYR 0.019 0.003 TYR A 311 ARG 0.006 0.001 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 106 time to evaluate : 1.089 Fit side-chains REVERT: A 135 ARG cc_start: 0.7818 (ptm-80) cc_final: 0.7579 (ptt180) REVERT: A 191 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7097 (mmp-170) REVERT: A 717 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: A 774 ILE cc_start: 0.8582 (mt) cc_final: 0.8245 (mp) REVERT: A 928 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7205 (mp10) outliers start: 60 outliers final: 34 residues processed: 156 average time/residue: 1.0048 time to fit residues: 170.7021 Evaluate side-chains 145 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 386 ASN A1022 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9564 Z= 0.196 Angle : 0.832 30.080 12968 Z= 0.358 Chirality : 0.043 0.273 1465 Planarity : 0.004 0.069 1612 Dihedral : 8.848 90.329 1387 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.01 % Allowed : 24.58 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.18 % 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: -1.99 (0.24), residues: 1129 helix: -0.65 (0.23), residues: 502 sheet: -0.44 (0.44), residues: 160 loop : -2.36 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS A 864 PHE 0.015 0.001 PHE A 894 TYR 0.015 0.001 TYR A 324 ARG 0.004 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 110 time to evaluate : 1.076 Fit side-chains REVERT: A 44 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7337 (ttt90) REVERT: A 191 ARG cc_start: 0.7668 (mmm160) cc_final: 0.7031 (mmp-170) REVERT: A 252 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8322 (mmtt) REVERT: A 385 ILE cc_start: 0.8232 (pt) cc_final: 0.7977 (pt) REVERT: A 717 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 774 ILE cc_start: 0.8517 (mt) cc_final: 0.8162 (mp) REVERT: A 926 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8094 (pp) REVERT: A 928 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: C 184 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6135 (pm20) REVERT: C 238 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7793 (pttp) outliers start: 51 outliers final: 25 residues processed: 150 average time/residue: 1.1650 time to fit residues: 189.9273 Evaluate side-chains 139 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9564 Z= 0.209 Angle : 0.828 30.714 12968 Z= 0.355 Chirality : 0.043 0.248 1465 Planarity : 0.004 0.067 1612 Dihedral : 8.340 88.255 1386 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.42 % Allowed : 25.86 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.72 (0.25), residues: 1129 helix: -0.41 (0.23), residues: 501 sheet: -0.21 (0.44), residues: 159 loop : -2.26 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.015 0.001 PHE C 108 TYR 0.013 0.001 TYR A 318 ARG 0.006 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 1.041 Fit side-chains REVERT: A 191 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7041 (mmp-170) REVERT: A 385 ILE cc_start: 0.8196 (pt) cc_final: 0.7935 (pt) REVERT: A 774 ILE cc_start: 0.8444 (mt) cc_final: 0.8097 (mp) REVERT: A 926 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8124 (pp) REVERT: A 928 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: C 184 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: C 238 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7733 (pttp) outliers start: 45 outliers final: 23 residues processed: 155 average time/residue: 1.1400 time to fit residues: 190.6601 Evaluate side-chains 141 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 95 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9564 Z= 0.160 Angle : 0.813 29.954 12968 Z= 0.345 Chirality : 0.042 0.237 1465 Planarity : 0.004 0.065 1612 Dihedral : 7.793 85.114 1383 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.23 % Allowed : 26.65 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.40 (0.25), residues: 1129 helix: -0.13 (0.23), residues: 505 sheet: -0.09 (0.43), residues: 159 loop : -2.12 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE C 108 TYR 0.016 0.001 TYR A 324 ARG 0.006 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.043 Fit side-chains REVERT: A 385 ILE cc_start: 0.8150 (pt) cc_final: 0.7895 (pt) REVERT: A 774 ILE cc_start: 0.8396 (mt) cc_final: 0.8088 (mp) REVERT: A 926 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8115 (pp) REVERT: A 928 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: C 155 LYS cc_start: 0.8162 (mttp) cc_final: 0.7841 (pttm) REVERT: C 184 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5981 (pm20) REVERT: C 238 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7688 (pttp) REVERT: C 343 LEU cc_start: 0.7901 (pp) cc_final: 0.7685 (pt) outliers start: 43 outliers final: 21 residues processed: 157 average time/residue: 1.1417 time to fit residues: 193.2821 Evaluate side-chains 137 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0570 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9564 Z= 0.171 Angle : 0.816 30.154 12968 Z= 0.346 Chirality : 0.042 0.233 1465 Planarity : 0.004 0.064 1612 Dihedral : 7.672 82.698 1383 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.93 % Allowed : 27.73 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.26 (0.25), residues: 1129 helix: -0.02 (0.23), residues: 506 sheet: 0.10 (0.44), residues: 158 loop : -2.09 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.020 0.001 PHE A1075 TYR 0.013 0.001 TYR A 324 ARG 0.008 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 116 time to evaluate : 1.081 Fit side-chains REVERT: A 385 ILE cc_start: 0.8136 (pt) cc_final: 0.7867 (pt) REVERT: A 774 ILE cc_start: 0.8382 (mt) cc_final: 0.8061 (mp) REVERT: A 926 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 928 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: A 1003 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8362 (tp) REVERT: C 100 THR cc_start: 0.4770 (OUTLIER) cc_final: 0.4513 (t) REVERT: C 155 LYS cc_start: 0.8145 (mttp) cc_final: 0.7850 (pttm) REVERT: C 184 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: C 238 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7648 (pttp) REVERT: C 343 LEU cc_start: 0.7862 (pp) cc_final: 0.7660 (pt) outliers start: 40 outliers final: 23 residues processed: 145 average time/residue: 1.1499 time to fit residues: 179.8201 Evaluate side-chains 137 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9564 Z= 0.257 Angle : 0.843 31.207 12968 Z= 0.363 Chirality : 0.044 0.238 1465 Planarity : 0.004 0.064 1612 Dihedral : 7.901 83.168 1383 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 3.05 % Allowed : 28.61 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.33 (0.25), residues: 1129 helix: -0.15 (0.23), residues: 507 sheet: 0.23 (0.44), residues: 157 loop : -2.10 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 236 HIS 0.004 0.001 HIS A 929 PHE 0.015 0.002 PHE C 108 TYR 0.014 0.002 TYR A 747 ARG 0.010 0.000 ARG A 723 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.061 Fit side-chains REVERT: A 385 ILE cc_start: 0.8219 (pt) cc_final: 0.7926 (pt) REVERT: A 774 ILE cc_start: 0.8423 (mt) cc_final: 0.8100 (mp) REVERT: A 926 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 928 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: C 100 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4643 (t) REVERT: C 155 LYS cc_start: 0.8171 (mttp) cc_final: 0.7881 (pttp) REVERT: C 184 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6055 (pm20) REVERT: C 238 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7696 (pttp) REVERT: C 343 LEU cc_start: 0.7945 (pp) cc_final: 0.7725 (pt) outliers start: 31 outliers final: 21 residues processed: 136 average time/residue: 1.2332 time to fit residues: 181.2051 Evaluate side-chains 132 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.0060 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107864 restraints weight = 10047.429| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.84 r_work: 0.3019 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9564 Z= 0.151 Angle : 0.806 29.661 12968 Z= 0.340 Chirality : 0.042 0.231 1465 Planarity : 0.004 0.065 1612 Dihedral : 7.360 81.792 1383 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.95 % Allowed : 28.81 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.13 (0.25), residues: 1129 helix: 0.09 (0.24), residues: 507 sheet: 0.26 (0.44), residues: 159 loop : -2.09 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE C 108 TYR 0.016 0.001 TYR A 324 ARG 0.009 0.000 ARG A 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.28 seconds wall clock time: 68 minutes 54.93 seconds (4134.93 seconds total)