Starting phenix.real_space_refine on Sat Feb 17 21:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2024/7et1_31294_updated.pdb" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9994 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6440 2.51 5 N 1649 2.21 5 O 1848 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 PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10015 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7652 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 939} Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2100 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 240} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 138 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1, 'PCW': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Unusual residues: {'NAG': 5, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.94, per 1000 atoms: 0.59 Number of scatterers: 10015 At special positions: 0 Unit cell: (118.69, 92.96, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 66 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1848 8.00 N 1649 7.00 C 6440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " 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 NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 161 " " NAG B 304 " - " ASN B 221 " " NAG B 305 " - " ASN B 193 " " NAG B 306 " - " ASN B 146 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 44.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' 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 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 292 through 321 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.946A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.563A pdb=" N THR A 375 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU A 376 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 460 through 472 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 684 through 693 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 764 through 805 removed outlier: 3.577A pdb=" N ASN A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 791 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 4.506A pdb=" N THR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.554A pdb=" N ILE A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 805 " --> pdb=" O TYR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 825 through 833 removed outlier: 4.064A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 896 through 899 No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 917 through 945 Processing helix chain 'A' and resid 953 through 956 No H-bonds generated for 'chain 'A' and resid 953 through 956' Processing helix chain 'A' and resid 962 through 980 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 995 through 1021 Proline residue: A1001 - end of helix removed outlier: 4.904A pdb=" N PHE A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'B' and resid 34 through 65 Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.684A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 4.278A pdb=" N GLY B 127 " --> pdb=" O ALA B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 156 through 162 removed outlier: 6.313A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing sheet with id= A, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.121A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 262 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 236 removed outlier: 4.430A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 260 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS A 258 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.564A pdb=" N ILE A 739 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 623 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET A 697 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.712A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 563 through 569 removed outlier: 3.517A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 535 through 538 removed outlier: 6.945A pdb=" N LEU A 592 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 530 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE A 594 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE A 532 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 211 through 214 removed outlier: 3.622A pdb=" N ASP A 211 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 269 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 82 through 85 Processing sheet with id= I, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.520A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1176 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: 3.60 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3160 1.34 - 1.46: 1933 1.46 - 1.58: 5036 1.58 - 1.70: 6 1.70 - 1.82: 99 Bond restraints: 10234 Sorted by residual: bond pdb=" C11 PCW A1102 " pdb=" O3 PCW A1102 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C31 PCW A1103 " pdb=" O2 PCW A1103 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C31 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C31 PCW B 301 " pdb=" O2 PCW B 301 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 10229 not shown) Histogram of bond angle deviations from ideal: 89.33 - 107.36: 417 107.36 - 125.39: 13314 125.39 - 143.41: 155 143.41 - 161.44: 0 161.44 - 179.46: 2 Bond angle restraints: 13888 Sorted by residual: angle pdb=" F3 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 109.63 179.46 -69.83 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F1 ALF A1105 " pdb="AL ALF A1105 " pdb=" F2 ALF A1105 " ideal model delta sigma weight residual 108.68 177.50 -68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" F2 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 110.21 89.85 20.36 3.00e+00 1.11e-01 4.60e+01 angle pdb=" F1 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 109.02 89.33 19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F2 ALF A1105 " pdb="AL ALF A1105 " pdb=" F3 ALF A1105 " ideal model delta sigma weight residual 109.59 90.33 19.26 3.00e+00 1.11e-01 4.12e+01 ... (remaining 13883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 6011 34.08 - 68.17: 256 68.17 - 102.25: 15 102.25 - 136.33: 4 136.33 - 170.42: 1 Dihedral angle restraints: 6287 sinusoidal: 2660 harmonic: 3627 Sorted by residual: dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual -66.66 103.76 -170.42 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C33 PCW A1102 " pdb=" C31 PCW A1102 " pdb=" C32 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sinusoidal sigma weight residual 191.83 57.87 133.96 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" N PCW A1103 " pdb=" C4 PCW A1103 " pdb=" C5 PCW A1103 " pdb=" O4P PCW A1103 " ideal model delta sinusoidal sigma weight residual 293.34 164.18 129.16 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 6284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1501 0.112 - 0.223: 67 0.223 - 0.335: 3 0.335 - 0.446: 2 0.446 - 0.558: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 161 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 221 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C20 CLR A1106 " pdb=" C17 CLR A1106 " pdb=" C21 CLR A1106 " pdb=" C22 CLR A1106 " both_signs ideal model delta sigma weight residual False 2.59 2.25 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1571 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 161 " -0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN B 161 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 161 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 161 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 121 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 122 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 449 " -0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 450 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.043 5.00e-02 4.00e+02 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 59 2.58 - 3.22: 9465 3.22 - 3.86: 20035 3.86 - 4.50: 27677 4.50 - 5.14: 43651 Nonbonded interactions: 100887 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" F3 ALF A1105 " model vdw 1.936 2.120 nonbonded pdb=" OE2 GLU A 230 " pdb=" O HOH A1201 " model vdw 2.052 2.440 nonbonded pdb=" OD1 ASP A 726 " pdb="MG MG A1101 " model vdw 2.072 2.170 nonbonded pdb=" OD2 ASP A 385 " pdb=" F3 ALF A1105 " model vdw 2.078 2.390 nonbonded pdb=" OG1 THR A 235 " pdb=" NE ARG A 249 " model vdw 2.079 2.520 ... (remaining 100882 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.007 0.132 10234 Z= 0.443 Angle : 1.250 69.831 13888 Z= 0.537 Chirality : 0.055 0.558 1574 Planarity : 0.007 0.083 1768 Dihedral : 17.047 170.419 3940 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.19 % Allowed : 20.70 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1245 helix: 1.14 (0.21), residues: 573 sheet: -0.09 (0.39), residues: 145 loop : -0.22 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 401 HIS 0.008 0.002 HIS B 114 PHE 0.025 0.002 PHE A 300 TYR 0.020 0.002 TYR A 802 ARG 0.009 0.001 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7949 (m-30) cc_final: 0.7686 (m-30) REVERT: A 401 TRP cc_start: 0.8503 (t60) cc_final: 0.8270 (t60) REVERT: A 505 GLU cc_start: 0.7691 (tt0) cc_final: 0.6833 (tm-30) REVERT: A 532 ILE cc_start: 0.8744 (mt) cc_final: 0.7817 (mm) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 1.6048 time to fit residues: 227.4761 Evaluate side-chains 81 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10234 Z= 0.181 Angle : 0.763 31.794 13888 Z= 0.324 Chirality : 0.044 0.269 1574 Planarity : 0.005 0.045 1768 Dihedral : 11.026 160.684 1653 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.54 % Allowed : 20.88 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1245 helix: 1.68 (0.22), residues: 576 sheet: 0.25 (0.40), residues: 146 loop : -0.03 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.004 0.001 HIS A 502 PHE 0.015 0.001 PHE A 300 TYR 0.009 0.001 TYR B 217 ARG 0.008 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 505 GLU cc_start: 0.7715 (tt0) cc_final: 0.6954 (tm-30) REVERT: A 537 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7562 (mp) outliers start: 27 outliers final: 6 residues processed: 97 average time/residue: 1.5103 time to fit residues: 156.5987 Evaluate side-chains 78 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8488 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.180 Angle : 0.746 30.795 13888 Z= 0.311 Chirality : 0.043 0.235 1574 Planarity : 0.004 0.039 1768 Dihedral : 10.637 161.814 1653 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.16 % Allowed : 20.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1245 helix: 1.79 (0.22), residues: 576 sheet: 0.04 (0.38), residues: 158 loop : 0.07 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.007 0.001 HIS A 512 PHE 0.015 0.001 PHE A 300 TYR 0.009 0.001 TYR B 217 ARG 0.005 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 505 GLU cc_start: 0.7711 (tt0) cc_final: 0.7010 (tm-30) outliers start: 23 outliers final: 10 residues processed: 92 average time/residue: 1.5459 time to fit residues: 151.4308 Evaluate side-chains 72 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 415 GLN A 706 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10234 Z= 0.166 Angle : 0.736 30.615 13888 Z= 0.304 Chirality : 0.043 0.215 1574 Planarity : 0.004 0.038 1768 Dihedral : 10.289 162.260 1653 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 20.70 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1245 helix: 1.89 (0.22), residues: 576 sheet: 0.04 (0.39), residues: 159 loop : 0.12 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 899 HIS 0.005 0.001 HIS A 512 PHE 0.015 0.001 PHE A 300 TYR 0.009 0.001 TYR B 217 ARG 0.007 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7902 (pt0) REVERT: A 505 GLU cc_start: 0.7704 (tt0) cc_final: 0.7060 (tm-30) REVERT: B 285 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8311 (mtmm) outliers start: 24 outliers final: 8 residues processed: 90 average time/residue: 1.5367 time to fit residues: 147.4067 Evaluate side-chains 77 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10234 Z= 0.154 Angle : 0.729 30.524 13888 Z= 0.299 Chirality : 0.042 0.205 1574 Planarity : 0.004 0.038 1768 Dihedral : 9.852 161.226 1653 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.88 % Allowed : 21.07 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1245 helix: 2.08 (0.22), residues: 562 sheet: 0.06 (0.38), residues: 159 loop : 0.15 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 899 HIS 0.004 0.001 HIS A 512 PHE 0.013 0.001 PHE A 300 TYR 0.009 0.001 TYR A 878 ARG 0.007 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: A 505 GLU cc_start: 0.7686 (tt0) cc_final: 0.7046 (tm-30) outliers start: 20 outliers final: 9 residues processed: 84 average time/residue: 1.5881 time to fit residues: 141.9279 Evaluate side-chains 72 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10234 Z= 0.279 Angle : 0.765 31.939 13888 Z= 0.322 Chirality : 0.044 0.188 1574 Planarity : 0.004 0.037 1768 Dihedral : 9.981 157.891 1653 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.88 % Allowed : 21.17 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1245 helix: 1.87 (0.22), residues: 568 sheet: 0.03 (0.37), residues: 168 loop : 0.12 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 799 HIS 0.005 0.001 HIS A 903 PHE 0.018 0.001 PHE A 300 TYR 0.011 0.001 TYR B 217 ARG 0.005 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: A 505 GLU cc_start: 0.7682 (tt0) cc_final: 0.7063 (tm-30) outliers start: 20 outliers final: 9 residues processed: 80 average time/residue: 1.5959 time to fit residues: 136.3856 Evaluate side-chains 71 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10234 Z= 0.149 Angle : 0.731 30.208 13888 Z= 0.300 Chirality : 0.042 0.209 1574 Planarity : 0.004 0.037 1768 Dihedral : 9.634 159.733 1653 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.69 % Allowed : 21.26 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1245 helix: 2.00 (0.22), residues: 566 sheet: 0.06 (0.36), residues: 173 loop : 0.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 899 HIS 0.004 0.001 HIS A 512 PHE 0.015 0.001 PHE A 300 TYR 0.010 0.001 TYR A 878 ARG 0.012 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: A 505 GLU cc_start: 0.7683 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 516 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6810 (ttt) outliers start: 18 outliers final: 7 residues processed: 76 average time/residue: 1.6462 time to fit residues: 133.1639 Evaluate side-chains 72 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.0030 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10234 Z= 0.204 Angle : 0.748 31.239 13888 Z= 0.309 Chirality : 0.043 0.186 1574 Planarity : 0.004 0.038 1768 Dihedral : 9.557 157.729 1653 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.88 % Allowed : 21.35 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1245 helix: 1.95 (0.22), residues: 568 sheet: 0.05 (0.37), residues: 168 loop : 0.11 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 799 HIS 0.004 0.001 HIS B 227 PHE 0.016 0.001 PHE A 300 TYR 0.009 0.001 TYR B 217 ARG 0.009 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: A 505 GLU cc_start: 0.7691 (tt0) cc_final: 0.7103 (tm-30) REVERT: A 516 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6809 (ttt) REVERT: B 34 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8048 (mm) outliers start: 20 outliers final: 9 residues processed: 83 average time/residue: 1.6738 time to fit residues: 147.6202 Evaluate side-chains 73 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10234 Z= 0.151 Angle : 0.741 30.328 13888 Z= 0.302 Chirality : 0.042 0.191 1574 Planarity : 0.004 0.048 1768 Dihedral : 9.295 158.653 1653 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.60 % Allowed : 21.64 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1245 helix: 2.04 (0.22), residues: 566 sheet: 0.16 (0.37), residues: 173 loop : 0.11 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 899 HIS 0.003 0.001 HIS A 512 PHE 0.014 0.001 PHE A 300 TYR 0.010 0.001 TYR A 878 ARG 0.011 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: A 505 GLU cc_start: 0.7699 (tt0) cc_final: 0.7113 (tm-30) REVERT: A 516 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6746 (ttt) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 1.6992 time to fit residues: 135.5108 Evaluate side-chains 70 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10234 Z= 0.233 Angle : 0.761 31.547 13888 Z= 0.317 Chirality : 0.044 0.180 1574 Planarity : 0.004 0.041 1768 Dihedral : 9.387 156.283 1653 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.22 % Allowed : 22.11 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1245 helix: 1.90 (0.22), residues: 570 sheet: 0.18 (0.37), residues: 173 loop : 0.09 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 799 HIS 0.004 0.001 HIS B 227 PHE 0.017 0.001 PHE A 300 TYR 0.009 0.001 TYR B 217 ARG 0.012 0.001 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: A 505 GLU cc_start: 0.7723 (tt0) cc_final: 0.7166 (tm-30) REVERT: B 34 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8073 (mm) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 1.6641 time to fit residues: 124.5084 Evaluate side-chains 68 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065840 restraints weight = 18029.710| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.47 r_work: 0.2748 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10234 Z= 0.296 Angle : 0.777 32.084 13888 Z= 0.329 Chirality : 0.045 0.181 1574 Planarity : 0.004 0.050 1768 Dihedral : 9.722 154.568 1653 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.51 % Allowed : 21.92 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1245 helix: 1.79 (0.22), residues: 571 sheet: 0.03 (0.37), residues: 168 loop : 0.05 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 543 HIS 0.005 0.001 HIS A 903 PHE 0.019 0.001 PHE A 300 TYR 0.011 0.001 TYR B 217 ARG 0.013 0.001 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.34 seconds wall clock time: 65 minutes 5.00 seconds (3905.00 seconds total)