Starting phenix.real_space_refine on Wed Apr 10 08:42:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucv_42141/04_2024/8ucv_42141_trim_updated.pdb" } resolution = 3.81 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 70 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 6062 2.51 5 N 1686 2.21 5 O 1980 1.98 5 H 9226 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1024": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19076 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 13976 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 822} Chain breaks: 2 Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3004 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "C" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1139 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 916 Unusual residues: {'DOC': 1, 'GTP': 1} Classifications: {'DNA': 19, 'RNA': 8, 'undetermined': 2} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 26, None: 2} Not linked: pdbres="GTP D 1 " pdbres=" G D 2 " Not linked: pdbres=" DG D 28 " pdbres="DOC D 29 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15568 SG CYS B 373 63.379 26.300 27.815 1.00204.55 S ATOM 15816 SG CYS B 390 58.069 24.200 31.577 1.00193.36 S ATOM 16468 SG CYS B 430 58.694 23.031 25.275 1.00231.52 S ATOM 14227 SG CYS B 293 57.457 28.897 27.301 1.00194.18 S Time building chain proxies: 9.51, per 1000 atoms: 0.50 Number of scatterers: 19076 At special positions: 0 Unit cell: (115.893, 118.08, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 46 16.00 P 70 15.00 Mg 2 11.99 O 1980 8.00 N 1686 7.00 C 6062 6.00 H 9226 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.66 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 430 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 293 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 373 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 390 " Number of angles added : 12 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 6 sheets defined 43.5% alpha, 12.6% beta 27 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 11.27 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 785 through 799 removed outlier: 3.544A pdb=" N ASN A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 926 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.043A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 4.191A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1082 through 1096 Processing helix chain 'A' and resid 1101 through 1121 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1210 Processing helix chain 'A' and resid 1213 through 1219 Processing helix chain 'A' and resid 1228 through 1234 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'B' and resid 279 through 287 removed outlier: 4.036A pdb=" N ASP B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.535A pdb=" N LYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.975A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 450 through 461 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.942A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 345 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 367 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 372 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 387 removed outlier: 3.520A pdb=" N VAL A 455 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.176A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 549 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASN A 555 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.623A pdb=" N ALA A1052 " --> pdb=" O LEU A1044 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1034 through 1040 removed outlier: 6.904A pdb=" N LEU A 857 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A1039 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 855 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 996 " --> pdb=" O MET A1003 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A1005 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 994 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1133 360 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 18.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 9209 1.13 - 1.42: 4237 1.42 - 1.71: 5904 1.71 - 2.00: 63 2.00 - 2.28: 12 Bond restraints: 19425 Sorted by residual: bond pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " ideal model delta sigma weight residual 1.284 1.542 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C4' DOC D 29 " pdb=" C3' DOC D 29 " ideal model delta sigma weight residual 1.334 1.548 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.448 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" O4' DOC D 29 " pdb=" C1' DOC D 29 " ideal model delta sigma weight residual 1.268 1.438 -0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4 DGT A1501 " pdb=" N3 DGT A1501 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.00e-02 2.50e+03 6.97e+01 ... (remaining 19420 not shown) Histogram of bond angle deviations from ideal: 73.51 - 85.69: 12 85.69 - 97.86: 0 97.86 - 110.04: 17246 110.04 - 122.21: 15006 122.21 - 134.39: 2933 Bond angle restraints: 35197 Sorted by residual: angle pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" C4' GTP D 1 " ideal model delta sigma weight residual 111.00 98.64 12.36 3.00e+00 1.11e-01 1.70e+01 angle pdb=" PB GTP D 1 " pdb=" O3B GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 120.50 132.38 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" C4' DC C 34 " pdb=" O4' DC C 34 " pdb=" C1' DC C 34 " ideal model delta sigma weight residual 109.70 103.94 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " ideal model delta sigma weight residual 111.00 100.09 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" OP1 DOC D 29 " pdb=" P DOC D 29 " pdb=" OP2 DOC D 29 " ideal model delta sigma weight residual 109.57 119.82 -10.25 3.00e+00 1.11e-01 1.17e+01 ... (remaining 35192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 8254 31.05 - 62.10: 622 62.10 - 93.16: 33 93.16 - 124.21: 5 124.21 - 155.26: 2 Dihedral angle restraints: 8916 sinusoidal: 5271 harmonic: 3645 Sorted by residual: dihedral pdb=" C4' GTP D 1 " pdb=" C5' GTP D 1 " pdb=" O5' GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual 260.87 105.61 155.26 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O5' GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PA GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sinusoidal sigma weight residual 274.12 142.07 132.05 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" O3B GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual -68.92 54.87 -123.79 1 2.00e+01 2.50e-03 3.73e+01 ... (remaining 8913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1399 0.070 - 0.140: 164 0.140 - 0.211: 4 0.211 - 0.281: 1 0.281 - 0.351: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C3' DGT A1501 " pdb=" C2' DGT A1501 " pdb=" C4' DGT A1501 " pdb=" O3' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.78 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C2' GTP D 1 " pdb=" C1' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" O2' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.79 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C4' GTP D 1 " pdb=" O3' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1567 not shown) Planarity restraints: 2608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 34 " -0.025 2.00e-02 2.50e+03 1.27e-02 4.44e+00 pdb=" N1 DC C 34 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DC C 34 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DC C 34 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DC C 34 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 34 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC C 34 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC C 34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC C 34 " 0.001 2.00e-02 2.50e+03 pdb=" H5 DC C 34 " -0.002 2.00e-02 2.50e+03 pdb=" H6 DC C 34 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 43 " -0.018 2.00e-02 2.50e+03 8.76e-03 2.30e+00 pdb=" N1 DT C 43 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT C 43 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DT C 43 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT C 43 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 43 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT C 43 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT C 43 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 43 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 43 " -0.000 2.00e-02 2.50e+03 pdb=" H3 DT C 43 " -0.003 2.00e-02 2.50e+03 pdb=" H6 DT C 43 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 806 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 807 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.016 5.00e-02 4.00e+02 ... (remaining 2605 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 383 2.10 - 2.72: 31497 2.72 - 3.35: 55302 3.35 - 3.97: 70731 3.97 - 4.60: 109007 Nonbonded interactions: 266920 Sorted by model distance: nonbonded pdb=" O LEU B 301 " pdb=" H HIS B 305 " model vdw 1.474 1.850 nonbonded pdb=" OD1 ASN A 931 " pdb=" H LEU A 934 " model vdw 1.527 1.850 nonbonded pdb="HH21 ARG A 392 " pdb=" O GLY A 470 " model vdw 1.542 1.850 nonbonded pdb=" O SER A 587 " pdb=" HH TYR A 732 " model vdw 1.556 1.850 nonbonded pdb=" O GLY A 840 " pdb="HH11 ARG A 977 " model vdw 1.591 1.850 ... (remaining 266915 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 6.620 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 81.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.008 0.258 10199 Z= 0.394 Angle : 0.600 12.359 14098 Z= 0.313 Chirality : 0.044 0.351 1570 Planarity : 0.003 0.029 1567 Dihedral : 20.558 155.258 4017 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 16.88 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.27), residues: 1046 helix: 1.72 (0.24), residues: 497 sheet: 0.54 (0.43), residues: 148 loop : 0.33 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.004 0.001 HIS B 309 PHE 0.007 0.001 PHE A 679 TYR 0.008 0.001 TYR A 425 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 741 MET cc_start: 0.8598 (tmm) cc_final: 0.8347 (tmm) REVERT: A 742 LEU cc_start: 0.9401 (tp) cc_final: 0.9081 (tt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.7924 time to fit residues: 105.4399 Evaluate side-chains 65 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN A 982 HIS A1068 GLN B 425 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10199 Z= 0.392 Angle : 0.638 8.485 14098 Z= 0.345 Chirality : 0.044 0.207 1570 Planarity : 0.004 0.034 1567 Dihedral : 20.055 165.538 1893 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.85 % Allowed : 18.15 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.98 (0.26), residues: 1046 helix: 1.38 (0.23), residues: 505 sheet: 0.18 (0.41), residues: 146 loop : 0.02 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 366 HIS 0.005 0.001 HIS B 309 PHE 0.015 0.002 PHE A 430 TYR 0.014 0.002 TYR A 706 ARG 0.003 0.001 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 741 MET cc_start: 0.8652 (tmm) cc_final: 0.8396 (tmm) REVERT: A 742 LEU cc_start: 0.9448 (tp) cc_final: 0.9186 (tt) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.7883 time to fit residues: 66.8944 Evaluate side-chains 59 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 985 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10199 Z= 0.186 Angle : 0.529 8.554 14098 Z= 0.288 Chirality : 0.041 0.174 1570 Planarity : 0.003 0.047 1567 Dihedral : 19.779 166.692 1893 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.49 % Allowed : 18.15 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.27), residues: 1046 helix: 1.65 (0.24), residues: 506 sheet: 0.42 (0.42), residues: 146 loop : 0.24 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.005 0.001 HIS B 309 PHE 0.007 0.001 PHE A 362 TYR 0.009 0.001 TYR B 387 ARG 0.006 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 LEU cc_start: 0.9439 (tp) cc_final: 0.9207 (tt) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 0.7447 time to fit residues: 67.3858 Evaluate side-chains 62 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS A 982 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10199 Z= 0.326 Angle : 0.589 8.244 14098 Z= 0.320 Chirality : 0.042 0.199 1570 Planarity : 0.004 0.036 1567 Dihedral : 19.665 160.516 1893 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.70 % Allowed : 17.94 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.03 (0.27), residues: 1046 helix: 1.41 (0.23), residues: 505 sheet: 0.16 (0.42), residues: 145 loop : 0.08 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 366 HIS 0.010 0.001 HIS A 982 PHE 0.014 0.001 PHE A 430 TYR 0.011 0.001 TYR A 953 ARG 0.004 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 GLU cc_start: 0.8629 (mp0) cc_final: 0.8368 (mp0) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.7006 time to fit residues: 63.0615 Evaluate side-chains 67 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS A 991 ASN A1099 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10199 Z= 0.401 Angle : 0.648 8.929 14098 Z= 0.355 Chirality : 0.043 0.228 1570 Planarity : 0.004 0.042 1567 Dihedral : 19.865 164.775 1893 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.02 % Allowed : 19.11 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.36 (0.26), residues: 1046 helix: 0.89 (0.23), residues: 504 sheet: -0.35 (0.42), residues: 149 loop : -0.20 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 366 HIS 0.007 0.001 HIS B 309 PHE 0.016 0.002 PHE A 430 TYR 0.017 0.002 TYR B 387 ARG 0.006 0.001 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 327 GLU cc_start: 0.8706 (mp0) cc_final: 0.8437 (mp0) outliers start: 19 outliers final: 17 residues processed: 70 average time/residue: 0.6944 time to fit residues: 64.3079 Evaluate side-chains 68 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 48 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10199 Z= 0.209 Angle : 0.551 8.743 14098 Z= 0.299 Chirality : 0.041 0.181 1570 Planarity : 0.004 0.034 1567 Dihedral : 19.712 168.488 1893 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.34 % Allowed : 19.21 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.95 (0.27), residues: 1046 helix: 1.44 (0.24), residues: 496 sheet: -0.16 (0.42), residues: 152 loop : 0.06 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.006 0.001 HIS B 309 PHE 0.010 0.001 PHE B 392 TYR 0.013 0.001 TYR B 387 ARG 0.004 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 GLU cc_start: 0.8759 (mp0) cc_final: 0.8489 (mp0) outliers start: 22 outliers final: 18 residues processed: 70 average time/residue: 0.7154 time to fit residues: 65.8795 Evaluate side-chains 69 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 425 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10199 Z= 0.313 Angle : 0.581 8.532 14098 Z= 0.318 Chirality : 0.042 0.192 1570 Planarity : 0.004 0.034 1567 Dihedral : 19.684 170.785 1893 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.34 % Allowed : 19.21 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.82 (0.27), residues: 1046 helix: 1.32 (0.24), residues: 497 sheet: -0.28 (0.42), residues: 149 loop : 0.04 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.005 0.001 HIS B 309 PHE 0.011 0.001 PHE A 796 TYR 0.010 0.001 TYR B 387 ARG 0.004 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 GLU cc_start: 0.8775 (mp0) cc_final: 0.8511 (mp0) outliers start: 22 outliers final: 19 residues processed: 70 average time/residue: 0.6721 time to fit residues: 62.4457 Evaluate side-chains 68 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 425 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10199 Z= 0.170 Angle : 0.531 8.669 14098 Z= 0.287 Chirality : 0.040 0.158 1570 Planarity : 0.004 0.033 1567 Dihedral : 19.574 175.564 1893 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.70 % Allowed : 19.85 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.27), residues: 1046 helix: 1.66 (0.24), residues: 497 sheet: -0.10 (0.42), residues: 148 loop : 0.24 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 333 HIS 0.005 0.001 HIS B 309 PHE 0.008 0.001 PHE B 392 TYR 0.011 0.001 TYR A 425 ARG 0.004 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 GLU cc_start: 0.8757 (mp0) cc_final: 0.8511 (mp0) outliers start: 16 outliers final: 13 residues processed: 62 average time/residue: 0.7055 time to fit residues: 57.9582 Evaluate side-chains 60 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 425 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10199 Z= 0.311 Angle : 0.579 8.360 14098 Z= 0.317 Chirality : 0.041 0.179 1570 Planarity : 0.004 0.055 1567 Dihedral : 19.616 177.319 1893 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.91 % Allowed : 19.75 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.90 (0.27), residues: 1046 helix: 1.38 (0.24), residues: 499 sheet: -0.33 (0.42), residues: 148 loop : 0.12 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.007 0.001 HIS B 309 PHE 0.011 0.001 PHE A 796 TYR 0.009 0.001 TYR A 414 ARG 0.005 0.001 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 953 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8856 (t80) REVERT: B 327 GLU cc_start: 0.8813 (mp0) cc_final: 0.8592 (mp0) outliers start: 18 outliers final: 17 residues processed: 63 average time/residue: 0.6638 time to fit residues: 56.2997 Evaluate side-chains 63 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10199 Z= 0.207 Angle : 0.544 8.646 14098 Z= 0.295 Chirality : 0.040 0.155 1570 Planarity : 0.004 0.045 1567 Dihedral : 19.582 179.807 1893 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.02 % Allowed : 19.96 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.11 (0.27), residues: 1046 helix: 1.54 (0.24), residues: 500 sheet: -0.25 (0.42), residues: 148 loop : 0.25 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.006 0.001 HIS B 309 PHE 0.009 0.001 PHE B 392 TYR 0.010 0.001 TYR A 425 ARG 0.009 0.000 ARG B 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 953 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8812 (t80) REVERT: B 327 GLU cc_start: 0.8805 (mp0) cc_final: 0.8585 (mp0) outliers start: 19 outliers final: 16 residues processed: 64 average time/residue: 0.6075 time to fit residues: 53.0096 Evaluate side-chains 63 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 790 TYR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.043907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.030255 restraints weight = 262396.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.031010 restraints weight = 142507.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.031488 restraints weight = 97030.879| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10199 Z= 0.138 Angle : 0.516 8.527 14098 Z= 0.277 Chirality : 0.039 0.135 1570 Planarity : 0.004 0.043 1567 Dihedral : 19.363 179.667 1893 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.27 % Allowed : 20.59 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.57 (0.27), residues: 1046 helix: 1.91 (0.24), residues: 500 sheet: 0.07 (0.44), residues: 142 loop : 0.44 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.006 0.001 HIS B 309 PHE 0.007 0.001 PHE B 285 TYR 0.011 0.001 TYR B 387 ARG 0.009 0.001 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4219.55 seconds wall clock time: 87 minutes 46.89 seconds (5266.89 seconds total)