Starting phenix.real_space_refine on Fri Dec 8 23:33:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/12_2023/7bsv_30168_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/12_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_30168/12_2023/7bsv_30168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/12_2023/7bsv_30168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/12_2023/7bsv_30168_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsv_30168/12_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-1.21rc1-5172/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: 3 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: 5.79, per 1000 atoms: 0.62 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: 4.22 Conformation dependent library (CDL) restraints added in 1.8 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: 2.49 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: 2.72 Time building geometry restraints manager: 4.47 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 - 22.67: 5128 22.67 - 45.35: 470 45.35 - 68.02: 89 68.02 - 90.70: 19 90.70 - 113.37: 7 Dihedral angle restraints: 5713 sinusoidal: 2368 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 5710 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: 0.850 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: 4.080 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.000 Find NCS groups from input model: 0.270 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.790 ------------------------------------------------------------------------------- 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 : 18.136 113.374 3546 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 : 0.985 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 21 residues processed: 195 average time/residue: 1.1258 time to fit residues: 235.8915 Evaluate side-chains 138 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.6487 time to fit residues: 3.6675 ------------------------------------------------------------------------------- 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 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: 0.8187 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9564 Z= 0.177 Angle : 0.875 29.255 12968 Z= 0.381 Chirality : 0.044 0.412 1465 Planarity : 0.005 0.060 1612 Dihedral : 10.274 98.227 1361 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.80 % Allowed : 22.81 % Favored : 71.39 % 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: -2.61 (0.18), residues: 502 sheet: -1.81 (0.39), residues: 164 loop : -2.87 (0.25), residues: 463 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 0.017 0.001 TYR A 324 ARG 0.005 0.000 ARG C 132 *********************** 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: 59 poor density : 132 time to evaluate : 1.103 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 20 residues processed: 179 average time/residue: 1.0945 time to fit residues: 211.5231 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.5292 time to fit residues: 3.1017 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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** A 777 GLN A 840 GLN A 872 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 0.041 9564 Z= 0.295 Angle : 0.872 31.085 12968 Z= 0.382 Chirality : 0.046 0.371 1465 Planarity : 0.005 0.073 1612 Dihedral : 9.702 90.627 1361 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 6.19 % Allowed : 22.22 % Favored : 71.58 % 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: -2.96 (0.23), residues: 1129 helix: -1.56 (0.21), residues: 504 sheet: -1.17 (0.40), residues: 166 loop : -2.63 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 236 HIS 0.005 0.001 HIS A 929 PHE 0.017 0.002 PHE C 108 TYR 0.017 0.002 TYR A 318 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 178 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 115 time to evaluate : 1.115 Fit side-chains outliers start: 63 outliers final: 33 residues processed: 172 average time/residue: 1.0846 time to fit residues: 201.8866 Evaluate side-chains 141 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.0996 time to fit residues: 1.6893 ------------------------------------------------------------------------------- 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: 0.0570 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 0.0370 chunk 90 optimal weight: 0.6980 overall best weight: 0.3094 ------------------------------------------------------------------------------- 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 A1022 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 254 ASN C 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9564 Z= 0.146 Angle : 0.810 29.736 12968 Z= 0.343 Chirality : 0.042 0.248 1465 Planarity : 0.004 0.072 1612 Dihedral : 8.573 88.910 1361 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.80 % Allowed : 23.30 % Favored : 70.89 % 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: -2.07 (0.24), residues: 1129 helix: -0.67 (0.22), residues: 510 sheet: -0.69 (0.43), residues: 159 loop : -2.38 (0.26), residues: 460 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 0.015 0.001 PHE C 108 TYR 0.017 0.001 TYR A 324 ARG 0.003 0.000 ARG C 132 *********************** 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 189 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 130 time to evaluate : 1.122 Fit side-chains outliers start: 59 outliers final: 28 residues processed: 181 average time/residue: 1.0288 time to fit residues: 202.8998 Evaluate side-chains 145 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.6223 time to fit residues: 2.8883 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 overall best weight: 2.6904 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8250 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9564 Z= 0.396 Angle : 0.889 33.145 12968 Z= 0.392 Chirality : 0.048 0.250 1465 Planarity : 0.005 0.069 1612 Dihedral : 8.931 88.025 1361 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 5.90 % Allowed : 24.48 % Favored : 69.62 % 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: -2.19 (0.24), residues: 1129 helix: -0.84 (0.22), residues: 503 sheet: -0.54 (0.42), residues: 166 loop : -2.45 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 236 HIS 0.006 0.001 HIS A 929 PHE 0.017 0.002 PHE C 108 TYR 0.018 0.002 TYR A 311 ARG 0.005 0.000 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 175 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 115 time to evaluate : 1.242 Fit side-chains outliers start: 60 outliers final: 31 residues processed: 163 average time/residue: 0.9981 time to fit residues: 177.2319 Evaluate side-chains 144 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 1.7232 time to fit residues: 3.4009 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN C 142 GLN C 144 ASN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2589 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= 0.188 Angle : 0.827 30.091 12968 Z= 0.353 Chirality : 0.044 0.302 1465 Planarity : 0.004 0.069 1612 Dihedral : 8.287 89.399 1361 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.11 % Allowed : 25.47 % Favored : 69.42 % 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: -1.76 (0.24), residues: 1129 helix: -0.45 (0.23), residues: 510 sheet: -0.28 (0.44), residues: 159 loop : -2.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 864 PHE 0.014 0.001 PHE A 894 TYR 0.013 0.001 TYR A 324 ARG 0.005 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 175 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 123 time to evaluate : 1.143 Fit side-chains outliers start: 52 outliers final: 30 residues processed: 168 average time/residue: 1.0750 time to fit residues: 196.2673 Evaluate side-chains 144 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 1.1023 time to fit residues: 2.7236 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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** C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2753 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= 0.180 Angle : 0.822 30.414 12968 Z= 0.350 Chirality : 0.043 0.244 1465 Planarity : 0.004 0.066 1612 Dihedral : 7.923 87.076 1361 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.51 % Allowed : 25.07 % Favored : 69.42 % 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: -1.48 (0.25), residues: 1129 helix: -0.21 (0.23), residues: 505 sheet: -0.11 (0.44), residues: 159 loop : -2.15 (0.27), residues: 465 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 324 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 177 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 1.133 Fit side-chains outliers start: 56 outliers final: 32 residues processed: 169 average time/residue: 0.9836 time to fit residues: 181.2070 Evaluate side-chains 148 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.8399 time to fit residues: 3.3552 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.2840 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 : 0.817 30.221 12968 Z= 0.346 Chirality : 0.043 0.238 1465 Planarity : 0.004 0.067 1612 Dihedral : 7.732 84.585 1361 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.33 % Allowed : 26.84 % 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: -1.36 (0.25), residues: 1129 helix: -0.12 (0.23), residues: 507 sheet: -0.01 (0.44), residues: 159 loop : -2.09 (0.27), residues: 463 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 0.015 0.001 PHE C 108 TYR 0.014 0.001 TYR A 324 ARG 0.005 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 161 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.185 Fit side-chains outliers start: 44 outliers final: 27 residues processed: 156 average time/residue: 1.0324 time to fit residues: 175.6298 Evaluate side-chains 138 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 1.1747 time to fit residues: 2.6482 ------------------------------------------------------------------------------- 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: 0.8980 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.2922 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= 0.188 Angle : 0.828 30.404 12968 Z= 0.351 Chirality : 0.043 0.233 1465 Planarity : 0.004 0.066 1612 Dihedral : 7.634 82.593 1361 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.93 % Allowed : 27.63 % Favored : 68.44 % 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: -1.29 (0.25), residues: 1129 helix: -0.08 (0.23), residues: 506 sheet: 0.06 (0.45), residues: 159 loop : -2.05 (0.27), residues: 464 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 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 158 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.044 Fit side-chains outliers start: 40 outliers final: 27 residues processed: 151 average time/residue: 1.0718 time to fit residues: 176.0633 Evaluate side-chains 141 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.8832 time to fit residues: 3.4699 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 0.0770 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3003 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= 0.166 Angle : 0.818 30.025 12968 Z= 0.345 Chirality : 0.042 0.230 1465 Planarity : 0.004 0.065 1612 Dihedral : 7.402 81.011 1361 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.15 % Allowed : 28.61 % Favored : 68.24 % 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: -1.15 (0.25), residues: 1129 helix: 0.03 (0.23), residues: 508 sheet: 0.17 (0.45), residues: 159 loop : -2.00 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE C 108 TYR 0.014 0.001 TYR A 324 ARG 0.009 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: 32 poor density : 111 time to evaluate : 1.174 Fit side-chains outliers start: 32 outliers final: 28 residues processed: 140 average time/residue: 1.0423 time to fit residues: 158.8467 Evaluate side-chains 135 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.1425 time to fit residues: 1.7454 ------------------------------------------------------------------------------- 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: 0.0050 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 A 769 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109189 restraints weight = 10012.113| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.85 r_work: 0.3013 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3150 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= 0.154 Angle : 0.812 29.855 12968 Z= 0.341 Chirality : 0.042 0.225 1465 Planarity : 0.004 0.065 1612 Dihedral : 7.098 79.395 1361 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.85 % Allowed : 28.81 % Favored : 68.34 % 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: -1.03 (0.25), residues: 1129 helix: 0.16 (0.24), residues: 510 sheet: 0.32 (0.45), residues: 159 loop : -2.02 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE C 108 TYR 0.014 0.001 TYR A 324 ARG 0.013 0.000 ARG A 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3871.94 seconds wall clock time: 69 minutes 34.56 seconds (4174.56 seconds total)