Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:02:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2022/6k7l_9939_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10615 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7893 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 961} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'BEF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.48, per 1000 atoms: 0.61 Number of scatterers: 10615 At special positions: 0 Unit cell: (73.04, 107.07, 166.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 54 16.00 Mg 1 11.99 F 3 9.00 O 1919 8.00 N 1756 7.00 C 6881 6.00 Be 1 4.00 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=2.04 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 9 sheets defined 42.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 61 through 75 removed outlier: 4.137A pdb=" N LEU A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 4.486A pdb=" N ARG A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 4.228A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 4.932A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 289 through 322 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 457 through 471 Proline residue: A 460 - end of helix removed outlier: 3.573A pdb=" N LEU A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 467 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 471 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 601 through 616 removed outlier: 3.892A pdb=" N THR A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 674 through 684 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 763 through 774 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.842A pdb=" N VAL A 791 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER A 792 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.681A pdb=" N LEU A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 830 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 855 removed outlier: 3.730A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 removed outlier: 3.897A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.914A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.580A pdb=" N LYS A 913 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN A 917 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 962 through 984 Processing helix chain 'A' and resid 990 through 1012 removed outlier: 4.047A pdb=" N SER A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1034 through 1061 removed outlier: 4.055A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.102A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' 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 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix 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 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.992A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.645A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 694 through 696 removed outlier: 3.948A pdb=" N ASP A 730 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 756 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 780 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 406 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 782 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER A 408 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 784 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 799 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLY A 785 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 801 " --> pdb=" O GLY A 785 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 817 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 514 through 517 Processing sheet with id= F, first strand: chain 'A' and resid 541 through 545 Processing sheet with id= G, first strand: chain 'A' and resid 419 through 424 removed outlier: 6.948A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.072A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 110 removed outlier: 4.749A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1137 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: 3.53 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1815 1.32 - 1.44: 2878 1.44 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10861 Sorted by residual: bond pdb=" BE BEF A1801 " pdb=" F2 BEF A1801 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" BE BEF A1801 " pdb=" F1 BEF A1801 " ideal model delta sigma weight residual 1.476 1.758 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" BE BEF A1801 " pdb=" F3 BEF A1801 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C ARG C 215 " pdb=" N ASN C 216 " ideal model delta sigma weight residual 1.329 1.218 0.111 1.86e-02 2.89e+03 3.53e+01 bond pdb=" CB VAL A 853 " pdb=" CG1 VAL A 853 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.79e+00 ... (remaining 10856 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.98: 160 103.98 - 111.64: 4521 111.64 - 119.29: 4442 119.29 - 126.94: 5468 126.94 - 134.59: 148 Bond angle restraints: 14739 Sorted by residual: angle pdb=" C LEU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" N SER A 223 " pdb=" CA SER A 223 " pdb=" C SER A 223 " ideal model delta sigma weight residual 109.81 120.43 -10.62 2.21e+00 2.05e-01 2.31e+01 angle pdb=" N SER A1024 " pdb=" CA SER A1024 " pdb=" C SER A1024 " ideal model delta sigma weight residual 112.38 117.89 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" C ILE A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 121.70 129.52 -7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C5 NAG C 404 " ideal model delta sigma weight residual 113.34 120.80 -7.46 1.74e+00 3.30e-01 1.84e+01 ... (remaining 14734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.47: 5803 19.47 - 38.95: 523 38.95 - 58.42: 91 58.42 - 77.89: 13 77.89 - 97.37: 11 Dihedral angle restraints: 6441 sinusoidal: 2602 harmonic: 3839 Sorted by residual: dihedral pdb=" CA ILE A 485 " pdb=" C ILE A 485 " pdb=" N TYR A 486 " pdb=" CA TYR A 486 " ideal model delta harmonic sigma weight residual -180.00 -130.47 -49.53 0 5.00e+00 4.00e-02 9.81e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual 180.00 -134.93 -45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA GLY A 336 " pdb=" C GLY A 336 " pdb=" N ALA A 337 " pdb=" CA ALA A 337 " ideal model delta harmonic sigma weight residual -180.00 -147.63 -32.37 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 6438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1259 0.071 - 0.142: 378 0.142 - 0.213: 39 0.213 - 0.284: 5 0.284 - 0.355: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILE A 485 " pdb=" CA ILE A 485 " pdb=" CG1 ILE A 485 " pdb=" CG2 ILE A 485 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1681 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.262 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C7 NAG C 405 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.132 2.00e-02 2.50e+03 1.14e-01 1.64e+02 pdb=" C7 NAG B 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.067 2.00e-02 2.50e+03 5.53e-02 3.82e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.011 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 71 2.56 - 3.15: 7948 3.15 - 3.73: 16867 3.73 - 4.32: 24834 4.32 - 4.90: 40220 Nonbonded interactions: 89940 Sorted by model distance: nonbonded pdb=" F3 BEF A1801 " pdb="MG MG A1802 " model vdw 1.976 2.120 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1802 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1802 " model vdw 2.096 2.170 nonbonded pdb=" O THR A 411 " pdb="MG MG A1802 " model vdw 2.132 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb=" F3 BEF A1801 " model vdw 2.187 2.390 ... (remaining 89935 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 54 5.16 5 Be 1 3.05 5 C 6881 2.51 5 N 1756 2.21 5 O 1919 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.810 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: 4.670 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 30.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.012 0.284 10861 Z= 0.814 Angle : 1.149 11.558 14739 Z= 0.624 Chirality : 0.066 0.355 1684 Planarity : 0.011 0.220 1841 Dihedral : 15.484 97.366 3956 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.46 % Favored : 92.31 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.27 (0.19), residues: 1301 helix: -2.16 (0.16), residues: 612 sheet: -0.76 (0.39), residues: 181 loop : -2.54 (0.23), residues: 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.273 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 1.2167 time to fit residues: 177.5223 Evaluate side-chains 96 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 147 HIS ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN A 323 HIS A 352 ASN A 381 HIS A 433 GLN A 765 GLN A 776 GLN A1118 HIS A1127 ASN C 36 GLN C 176 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10861 Z= 0.191 Angle : 0.635 8.937 14739 Z= 0.329 Chirality : 0.044 0.357 1684 Planarity : 0.005 0.068 1841 Dihedral : 8.163 110.123 1468 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.93 (0.22), residues: 1301 helix: -0.75 (0.19), residues: 616 sheet: -0.31 (0.39), residues: 189 loop : -2.26 (0.26), residues: 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.160 Fit side-chains outliers start: 23 outliers final: 6 residues processed: 126 average time/residue: 1.1099 time to fit residues: 152.7299 Evaluate side-chains 115 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.7608 time to fit residues: 4.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 0.0040 chunk 81 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 187 ASN A 455 ASN A 456 HIS A 679 ASN A 765 GLN A 776 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 10861 Z= 0.143 Angle : 0.559 7.951 14739 Z= 0.289 Chirality : 0.042 0.368 1684 Planarity : 0.004 0.061 1841 Dihedral : 7.423 110.931 1468 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.23), residues: 1301 helix: -0.01 (0.21), residues: 613 sheet: -0.07 (0.39), residues: 189 loop : -1.99 (0.26), residues: 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.230 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 125 average time/residue: 1.0298 time to fit residues: 140.9594 Evaluate side-chains 111 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4946 time to fit residues: 4.0098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 765 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 10861 Z= 0.150 Angle : 0.538 6.939 14739 Z= 0.279 Chirality : 0.042 0.373 1684 Planarity : 0.004 0.052 1841 Dihedral : 7.191 110.637 1468 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1301 helix: 0.35 (0.22), residues: 614 sheet: 0.05 (0.39), residues: 189 loop : -1.87 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.201 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 1.0939 time to fit residues: 147.5004 Evaluate side-chains 116 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1764 time to fit residues: 3.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 8.9990 chunk 71 optimal weight: 0.0040 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 776 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10861 Z= 0.244 Angle : 0.591 9.580 14739 Z= 0.305 Chirality : 0.045 0.382 1684 Planarity : 0.004 0.062 1841 Dihedral : 7.312 110.726 1468 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1301 helix: 0.35 (0.21), residues: 607 sheet: 0.11 (0.39), residues: 185 loop : -1.83 (0.26), residues: 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.238 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 128 average time/residue: 1.0789 time to fit residues: 151.3710 Evaluate side-chains 115 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1514 time to fit residues: 3.0360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.0070 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 10861 Z= 0.209 Angle : 0.575 8.367 14739 Z= 0.297 Chirality : 0.044 0.377 1684 Planarity : 0.004 0.066 1841 Dihedral : 7.231 110.649 1468 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1301 helix: 0.43 (0.22), residues: 603 sheet: 0.11 (0.40), residues: 186 loop : -1.75 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.363 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 121 average time/residue: 1.0720 time to fit residues: 142.6619 Evaluate side-chains 110 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1243 time to fit residues: 2.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 10861 Z= 0.152 Angle : 0.554 8.951 14739 Z= 0.283 Chirality : 0.042 0.372 1684 Planarity : 0.004 0.070 1841 Dihedral : 7.033 110.323 1468 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1301 helix: 0.66 (0.22), residues: 603 sheet: 0.21 (0.40), residues: 189 loop : -1.69 (0.26), residues: 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 120 average time/residue: 1.0323 time to fit residues: 136.3701 Evaluate side-chains 112 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1227 time to fit residues: 2.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 10861 Z= 0.161 Angle : 0.544 8.762 14739 Z= 0.280 Chirality : 0.042 0.373 1684 Planarity : 0.004 0.049 1841 Dihedral : 6.966 110.122 1468 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.70 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1301 helix: 0.76 (0.22), residues: 603 sheet: 0.23 (0.39), residues: 194 loop : -1.65 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 1.0581 time to fit residues: 139.9426 Evaluate side-chains 115 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1201 time to fit residues: 2.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.0670 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 10861 Z= 0.141 Angle : 0.531 9.027 14739 Z= 0.274 Chirality : 0.042 0.367 1684 Planarity : 0.004 0.049 1841 Dihedral : 6.854 109.763 1468 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1301 helix: 0.95 (0.22), residues: 607 sheet: 0.32 (0.40), residues: 186 loop : -1.68 (0.26), residues: 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 120 average time/residue: 1.0302 time to fit residues: 136.1793 Evaluate side-chains 114 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.6226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 0.0040 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 10861 Z= 0.167 Angle : 0.544 9.414 14739 Z= 0.280 Chirality : 0.042 0.377 1684 Planarity : 0.004 0.048 1841 Dihedral : 6.871 109.519 1468 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1301 helix: 0.92 (0.22), residues: 604 sheet: 0.38 (0.40), residues: 194 loop : -1.58 (0.27), residues: 503 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 1.0359 time to fit residues: 133.7264 Evaluate side-chains 112 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.4557 time to fit residues: 3.3296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 0.0980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.190153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.153237 restraints weight = 10066.100| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.29 r_work: 0.3197 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10861 Z= 0.235 Angle : 0.575 9.349 14739 Z= 0.297 Chirality : 0.044 0.381 1684 Planarity : 0.004 0.048 1841 Dihedral : 7.024 109.756 1468 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1301 helix: 0.72 (0.22), residues: 607 sheet: 0.48 (0.40), residues: 190 loop : -1.58 (0.27), residues: 504 =============================================================================== Job complete usr+sys time: 3245.41 seconds wall clock time: 58 minutes 50.09 seconds (3530.09 seconds total)