Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 19:39:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/10_2023/7bsv_30168_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/10_2023/7bsv_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_30168/10_2023/7bsv_30168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/10_2023/7bsv_30168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/10_2023/7bsv_30168_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/10_2023/7bsv_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-1.21rc1-5097/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 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 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: 5.56, 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: 3.99 Conformation dependent library (CDL) restraints added in 1.3 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: 1.95 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: 2.63 Time building geometry restraints manager: 4.30 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 - 20.35: 4961 20.35 - 40.70: 524 40.70 - 61.05: 112 61.05 - 81.40: 17 81.40 - 101.75: 7 Dihedral angle restraints: 5621 sinusoidal: 2276 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 5618 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: 1.240 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: 3.990 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.530 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.460 ------------------------------------------------------------------------------- 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 : 17.258 101.748 3454 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 *********************** 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 : 1.097 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 21 residues processed: 195 average time/residue: 1.1537 time to fit residues: 241.9082 Evaluate side-chains 138 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.6514 time to fit residues: 3.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 397 ASN A 764 GLN A 777 GLN A 819 ASN A 862 HIS A1022 ASN C 36 GLN C 129 GLN C 142 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 298 ASN ** C 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9564 Z= 0.172 Angle : 0.864 30.202 12968 Z= 0.376 Chirality : 0.045 0.523 1465 Planarity : 0.005 0.057 1612 Dihedral : 7.577 88.453 1269 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 6.00 % Allowed : 22.52 % Favored : 71.48 % 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: -4.03 (0.21), residues: 1129 helix: -2.66 (0.17), residues: 508 sheet: -1.81 (0.39), residues: 164 loop : -2.85 (0.25), residues: 457 *********************** 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 193 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 132 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 20 residues processed: 180 average time/residue: 1.0566 time to fit residues: 205.6017 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.4983 time to fit residues: 3.0409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A 840 GLN A 872 HIS A1022 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** C 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9564 Z= 0.317 Angle : 0.880 31.217 12968 Z= 0.387 Chirality : 0.047 0.386 1465 Planarity : 0.005 0.072 1612 Dihedral : 7.600 83.761 1269 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 6.29 % Allowed : 22.42 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -3.02 (0.22), residues: 1129 helix: -1.62 (0.20), residues: 504 sheet: -1.21 (0.40), residues: 166 loop : -2.65 (0.26), residues: 459 *********************** 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 179 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 115 time to evaluate : 1.056 Fit side-chains outliers start: 64 outliers final: 34 residues processed: 173 average time/residue: 1.0331 time to fit residues: 193.9432 Evaluate side-chains 140 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 1.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 29 optimal weight: 0.0030 chunk 90 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 A 777 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9564 Z= 0.164 Angle : 0.817 29.750 12968 Z= 0.348 Chirality : 0.043 0.301 1465 Planarity : 0.004 0.075 1612 Dihedral : 7.030 77.204 1269 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.29 % Allowed : 22.91 % Favored : 70.80 % 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: -2.10 (0.24), residues: 1129 helix: -0.70 (0.22), residues: 504 sheet: -0.65 (0.43), residues: 159 loop : -2.41 (0.26), residues: 466 *********************** 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 190 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 126 time to evaluate : 1.017 Fit side-chains outliers start: 64 outliers final: 30 residues processed: 179 average time/residue: 1.0189 time to fit residues: 197.6594 Evaluate side-chains 143 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.1229 time to fit residues: 2.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9564 Z= 0.449 Angle : 0.907 33.439 12968 Z= 0.403 Chirality : 0.049 0.310 1465 Planarity : 0.005 0.072 1612 Dihedral : 7.611 80.111 1269 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 6.49 % Allowed : 23.50 % Favored : 70.01 % 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: -2.28 (0.24), residues: 1129 helix: -0.95 (0.22), residues: 501 sheet: -0.56 (0.42), residues: 164 loop : -2.45 (0.26), residues: 464 *********************** 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 175 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 109 time to evaluate : 1.044 Fit side-chains outliers start: 66 outliers final: 34 residues processed: 164 average time/residue: 0.9662 time to fit residues: 173.0053 Evaluate side-chains 141 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 0.6663 time to fit residues: 2.9200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 ** 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: 0.8182 moved from start: 0.2602 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= 0.180 Angle : 0.821 29.873 12968 Z= 0.351 Chirality : 0.043 0.278 1465 Planarity : 0.004 0.072 1612 Dihedral : 7.113 76.949 1269 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.60 % Allowed : 24.39 % Favored : 70.01 % 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: -1.80 (0.24), residues: 1129 helix: -0.46 (0.23), residues: 501 sheet: -0.29 (0.44), residues: 159 loop : -2.32 (0.26), residues: 469 *********************** 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 175 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 118 time to evaluate : 1.000 Fit side-chains outliers start: 57 outliers final: 32 residues processed: 169 average time/residue: 0.9930 time to fit residues: 182.8528 Evaluate side-chains 137 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 1.5086 time to fit residues: 3.1008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 0.0270 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- 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** C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9564 Z= 0.214 Angle : 0.833 30.774 12968 Z= 0.357 Chirality : 0.044 0.258 1465 Planarity : 0.004 0.070 1612 Dihedral : 6.997 74.589 1269 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.92 % Allowed : 25.86 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -1.61 (0.25), residues: 1129 helix: -0.29 (0.23), residues: 504 sheet: -0.19 (0.44), residues: 160 loop : -2.25 (0.27), residues: 465 *********************** 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: 50 poor density : 114 time to evaluate : 1.063 Fit side-chains outliers start: 50 outliers final: 32 residues processed: 160 average time/residue: 1.0559 time to fit residues: 184.3427 Evaluate side-chains 144 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.1406 time to fit residues: 1.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9564 Z= 0.160 Angle : 0.812 29.886 12968 Z= 0.343 Chirality : 0.042 0.242 1465 Planarity : 0.004 0.069 1612 Dihedral : 6.703 69.535 1269 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.03 % Allowed : 27.14 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -1.35 (0.25), residues: 1129 helix: -0.07 (0.23), residues: 506 sheet: -0.08 (0.44), residues: 159 loop : -2.12 (0.27), residues: 464 *********************** 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 162 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.046 Fit side-chains outliers start: 41 outliers final: 27 residues processed: 156 average time/residue: 0.9800 time to fit residues: 166.2900 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.6144 time to fit residues: 2.7403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 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: 0.8146 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9564 Z= 0.176 Angle : 0.822 30.167 12968 Z= 0.349 Chirality : 0.043 0.233 1465 Planarity : 0.004 0.069 1612 Dihedral : 6.642 68.189 1269 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.44 % Allowed : 28.12 % Favored : 68.44 % 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: -1.28 (0.25), residues: 1129 helix: 0.00 (0.23), residues: 507 sheet: 0.03 (0.44), residues: 159 loop : -2.12 (0.27), residues: 463 *********************** 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 147 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 0.955 Fit side-chains outliers start: 35 outliers final: 31 residues processed: 141 average time/residue: 0.9920 time to fit residues: 152.4889 Evaluate side-chains 136 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.6527 time to fit residues: 2.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 142 GLN C 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9564 Z= 0.177 Angle : 0.821 30.146 12968 Z= 0.348 Chirality : 0.043 0.228 1465 Planarity : 0.004 0.068 1612 Dihedral : 6.621 66.792 1269 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.93 % Allowed : 27.53 % Favored : 68.53 % 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: -1.20 (0.25), residues: 1129 helix: 0.03 (0.23), residues: 508 sheet: 0.13 (0.44), residues: 159 loop : -2.08 (0.28), residues: 462 ********************** 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 146 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 1.120 Fit side-chains outliers start: 40 outliers final: 31 residues processed: 141 average time/residue: 0.9746 time to fit residues: 150.0286 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.8316 time to fit residues: 3.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 63 GLN A 215 GLN A 386 ASN C 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.144402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103530 restraints weight = 10138.300| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.82 r_work: 0.2929 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9564 Z= 0.292 Angle : 0.861 31.756 12968 Z= 0.372 Chirality : 0.045 0.232 1465 Planarity : 0.004 0.068 1612 Dihedral : 6.992 70.827 1269 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 3.34 % Allowed : 28.22 % Favored : 68.44 % 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: -1.37 (0.25), residues: 1129 helix: -0.16 (0.23), residues: 504 sheet: 0.12 (0.44), residues: 159 loop : -2.10 (0.27), residues: 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.62 seconds wall clock time: 66 minutes 24.99 seconds (3984.99 seconds total)