Starting phenix.real_space_refine (version: dev) on Thu Feb 23 10:53:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2023/7et1_31294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2023/7et1_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_2023/7et1_31294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2023/7et1_31294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2023/7et1_31294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et1_31294/02_2023/7et1_31294_updated.pdb" } resolution = 2.6 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= 0.002 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 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-4877/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 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: 6.88, per 1000 atoms: 0.69 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: 4.16 Conformation dependent library (CDL) restraints added in 1.4 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: 1.48 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: 3.48 Time building geometry restraints manager: 4.46 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: 5865 34.08 - 68.17: 241 68.17 - 102.25: 15 102.25 - 136.33: 4 136.33 - 170.42: 1 Dihedral angle restraints: 6126 sinusoidal: 2499 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 6123 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 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. 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.150 Process input model: 30.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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= 0.436 Angle : 1.246 69.831 13888 Z= 0.536 Chirality : 0.054 0.558 1574 Planarity : 0.007 0.083 1768 Dihedral : 17.100 170.419 3779 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 % 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 *********************** 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 : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 1.6878 time to fit residues: 239.1661 Evaluate side-chains 79 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 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: 0.8766 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10234 Z= 0.181 Angle : 0.760 31.538 13888 Z= 0.324 Chirality : 0.044 0.332 1574 Planarity : 0.005 0.046 1768 Dihedral : 10.530 160.370 1490 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 2.82 % 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: 1.16 (0.24), residues: 1245 helix: 1.69 (0.22), residues: 576 sheet: 0.26 (0.40), residues: 146 loop : -0.04 (0.27), residues: 523 *********************** 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 108 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 5 residues processed: 102 average time/residue: 1.5610 time to fit residues: 169.5185 Evaluate side-chains 75 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2388 time to fit residues: 1.9023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8790 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10234 Z= 0.175 Angle : 0.745 31.007 13888 Z= 0.311 Chirality : 0.043 0.246 1574 Planarity : 0.004 0.039 1768 Dihedral : 9.840 161.696 1490 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.45 % 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: 1.27 (0.24), residues: 1245 helix: 1.82 (0.22), residues: 576 sheet: 0.07 (0.39), residues: 156 loop : 0.05 (0.27), residues: 513 *********************** 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 96 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 1.170 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 93 average time/residue: 1.4731 time to fit residues: 146.3563 Evaluate side-chains 76 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1650 time to fit residues: 2.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8828 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10234 Z= 0.241 Angle : 0.755 31.520 13888 Z= 0.317 Chirality : 0.044 0.205 1574 Planarity : 0.004 0.039 1768 Dihedral : 9.806 158.114 1490 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.35 % 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: 1.28 (0.24), residues: 1245 helix: 1.83 (0.22), residues: 574 sheet: 0.01 (0.38), residues: 159 loop : 0.11 (0.27), residues: 512 *********************** 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: 25 poor density : 67 time to evaluate : 1.186 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 1.5226 time to fit residues: 143.2255 Evaluate side-chains 74 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1735 time to fit residues: 2.1691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 415 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10234 Z= 0.152 Angle : 0.726 30.327 13888 Z= 0.299 Chirality : 0.042 0.196 1574 Planarity : 0.004 0.038 1768 Dihedral : 9.424 159.429 1490 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.79 % 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: 1.99 (0.22), residues: 567 sheet: 0.13 (0.38), residues: 159 loop : 0.07 (0.27), residues: 519 *********************** 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 85 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 81 average time/residue: 1.5898 time to fit residues: 137.2815 Evaluate side-chains 70 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.2611 time to fit residues: 2.9112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 10234 Z= 0.375 Angle : 0.789 33.000 13888 Z= 0.339 Chirality : 0.046 0.176 1574 Planarity : 0.004 0.037 1768 Dihedral : 9.856 153.956 1490 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.26 % 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: 1.18 (0.24), residues: 1245 helix: 1.73 (0.22), residues: 568 sheet: 0.07 (0.36), residues: 168 loop : 0.04 (0.27), residues: 509 *********************** 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 87 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 82 average time/residue: 1.5981 time to fit residues: 140.0858 Evaluate side-chains 69 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.1818 time to fit residues: 2.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8826 moved from start: 0.2830 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= 0.161 Angle : 0.732 30.178 13888 Z= 0.303 Chirality : 0.042 0.185 1574 Planarity : 0.004 0.038 1768 Dihedral : 9.439 157.901 1490 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.51 % 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: 1.33 (0.24), residues: 1245 helix: 1.90 (0.22), residues: 570 sheet: 0.17 (0.37), residues: 168 loop : 0.04 (0.27), residues: 507 *********************** 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 79 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 1.5440 time to fit residues: 128.3664 Evaluate side-chains 70 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8827 moved from start: 0.2934 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= 0.173 Angle : 0.733 30.742 13888 Z= 0.303 Chirality : 0.042 0.177 1574 Planarity : 0.004 0.038 1768 Dihedral : 9.206 155.802 1490 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 1.60 % 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: 1.43 (0.24), residues: 1245 helix: 1.96 (0.22), residues: 569 sheet: 0.26 (0.37), residues: 168 loop : 0.11 (0.27), residues: 508 *********************** 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 78 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 1.175 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 1.5528 time to fit residues: 127.8433 Evaluate side-chains 69 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8819 moved from start: 0.3008 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= 0.157 Angle : 0.732 30.528 13888 Z= 0.300 Chirality : 0.042 0.178 1574 Planarity : 0.004 0.037 1768 Dihedral : 9.014 156.231 1490 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.51 % 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: 1.48 (0.24), residues: 1245 helix: 2.01 (0.22), residues: 568 sheet: 0.39 (0.38), residues: 163 loop : 0.10 (0.27), residues: 514 *********************** 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 75 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 1.5693 time to fit residues: 125.8623 Evaluate side-chains 68 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.5536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8851 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10234 Z= 0.236 Angle : 0.753 31.493 13888 Z= 0.315 Chirality : 0.043 0.176 1574 Planarity : 0.004 0.039 1768 Dihedral : 9.171 153.631 1490 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.13 % 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: 1.87 (0.22), residues: 572 sheet: 0.28 (0.37), residues: 168 loop : 0.11 (0.27), residues: 505 ********************** 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 71 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 1.127 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 1.6231 time to fit residues: 123.2639 Evaluate side-chains 66 residues out of total 1063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.067764 restraints weight = 18043.344| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.38 r_work: 0.2818 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10234 Z= 0.220 Angle : 0.748 31.262 13888 Z= 0.311 Chirality : 0.043 0.176 1574 Planarity : 0.004 0.045 1768 Dihedral : 9.177 154.469 1490 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.22 % 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: 1.34 (0.24), residues: 1245 helix: 1.85 (0.22), residues: 573 sheet: 0.27 (0.36), residues: 168 loop : 0.08 (0.27), residues: 504 =============================================================================== Job complete usr+sys time: 3442.06 seconds wall clock time: 62 minutes 5.88 seconds (3725.88 seconds total)