Starting phenix.real_space_refine on Mon Apr 8 15:08:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/04_2024/8sny_40642.pdb" } resolution = 3.41 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 75 5.16 5 C 8733 2.51 5 N 2333 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 11317 Classifications: {'peptide': 1388} Link IDs: {'PTRANS': 47, 'TRANS': 1340} Chain breaks: 3 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 1 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Time building chain proxies: 7.59, per 1000 atoms: 0.55 Number of scatterers: 13744 At special positions: 0 Unit cell: (123.786, 108.974, 108.974, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 8 15.00 O 2595 8.00 N 2333 7.00 C 8733 6.00 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=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.6 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.725A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.679A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.813A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.782A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 380 removed outlier: 3.535A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.966A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.766A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.935A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.449A pdb=" N GLY A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.583A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.399A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 3.776A pdb=" N ASN A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 659 Proline residue: A 656 - end of helix removed outlier: 3.777A pdb=" N LEU A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.959A pdb=" N PHE A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 removed outlier: 4.718A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.743A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.538A pdb=" N PHE A 985 " --> pdb=" O PRO A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.300A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.719A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1110 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.861A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 4.256A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.514A pdb=" N CYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1458 through 1461 removed outlier: 3.952A pdb=" N LEU A1461 " --> pdb=" O GLU A1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.570A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 157 removed outlier: 4.798A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 183 Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.570A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 4.050A pdb=" N ARG E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 191 through 200 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.319A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.543A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.845A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1364 750 hydrogen bonds defined for protein. 2178 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: 5.04 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2265 1.31 - 1.44: 3591 1.44 - 1.56: 8000 1.56 - 1.69: 15 1.69 - 1.81: 127 Bond restraints: 13998 Sorted by residual: bond pdb=" CA PHE A 704 " pdb=" C PHE A 704 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA MET A 631 " pdb=" C MET A 631 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.24e-02 6.50e+03 2.50e+01 bond pdb=" CA LYS A1145 " pdb=" C LYS A1145 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 1.522 1.463 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.66e+01 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.40: 205 104.40 - 111.86: 6878 111.86 - 119.32: 4906 119.32 - 126.77: 6810 126.77 - 134.23: 147 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N LEU A 667 " pdb=" CA LEU A 667 " pdb=" C LEU A 667 " ideal model delta sigma weight residual 111.02 98.88 12.14 1.22e+00 6.72e-01 9.90e+01 angle pdb=" N ALA A 675 " pdb=" CA ALA A 675 " pdb=" C ALA A 675 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 112.90 103.68 9.22 1.31e+00 5.83e-01 4.95e+01 angle pdb=" N LYS A1025 " pdb=" CA LYS A1025 " pdb=" C LYS A1025 " ideal model delta sigma weight residual 114.04 105.99 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta sigma weight residual 110.79 100.65 10.14 1.66e+00 3.63e-01 3.73e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7570 17.83 - 35.66: 811 35.66 - 53.49: 153 53.49 - 71.32: 36 71.32 - 89.15: 14 Dihedral angle restraints: 8584 sinusoidal: 3627 harmonic: 4957 Sorted by residual: dihedral pdb=" C PHE A 704 " pdb=" N PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual -122.60 -108.68 -13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N PHE A 704 " pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual 122.80 112.96 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" CA GLN A 874 " pdb=" C GLN A 874 " pdb=" N HIS A 875 " pdb=" CA HIS A 875 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1847 0.055 - 0.110: 310 0.110 - 0.166: 35 0.166 - 0.221: 7 0.221 - 0.276: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2198 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 707 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ALA A 707 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 707 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 708 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 53 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 54 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 83 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 84 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 116 2.53 - 3.12: 10875 3.12 - 3.71: 22625 3.71 - 4.31: 31221 4.31 - 4.90: 52711 Nonbonded interactions: 117548 Sorted by model distance: nonbonded pdb=" O ASN A 991 " pdb=" ND2 ASN A 991 " model vdw 1.932 2.520 nonbonded pdb=" O CYS A 251 " pdb=" OG1 THR A 264 " model vdw 2.216 2.440 nonbonded pdb=" OD1 ASP D 136 " pdb=" NH1 ARG E 134 " model vdw 2.242 2.520 nonbonded pdb=" NH2 ARG A 588 " pdb=" O LEU A1151 " model vdw 2.256 2.520 nonbonded pdb=" O VAL A1399 " pdb=" OG1 THR A1403 " model vdw 2.271 2.440 ... (remaining 117543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 184) selection = (chain 'C' and resid 130 through 184) } 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=0.20 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: 0.380 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: 0.020 Extract box with map and model: 2.530 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.900 Find NCS groups from input model: 0.380 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.065 13998 Z= 0.231 Angle : 0.625 12.136 18946 Z= 0.350 Chirality : 0.042 0.276 2201 Planarity : 0.004 0.049 2361 Dihedral : 15.353 89.155 5366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.33 % Allowed : 0.85 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.21), residues: 1662 helix: 1.75 (0.17), residues: 955 sheet: -1.69 (0.55), residues: 72 loop : -0.86 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 480 HIS 0.019 0.001 HIS C 150 PHE 0.024 0.001 PHE A 704 TYR 0.021 0.001 TYR A1356 ARG 0.009 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 1.332 Fit side-chains REVERT: A 669 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (pttp) REVERT: A 824 MET cc_start: 0.6091 (tmm) cc_final: 0.5831 (tmm) REVERT: A 1023 ASP cc_start: 0.6407 (m-30) cc_final: 0.6169 (t0) REVERT: B 152 LEU cc_start: 0.9017 (tp) cc_final: 0.8600 (tt) REVERT: C 140 GLU cc_start: 0.7632 (mp0) cc_final: 0.6963 (mp0) REVERT: C 177 MET cc_start: 0.8371 (tpp) cc_final: 0.8031 (tpp) REVERT: D 177 MET cc_start: 0.7450 (ppp) cc_final: 0.6904 (ppp) REVERT: D 178 ILE cc_start: 0.7151 (mm) cc_final: 0.6830 (mm) REVERT: E 145 ILE cc_start: 0.7918 (mt) cc_final: 0.7545 (mt) outliers start: 5 outliers final: 2 residues processed: 313 average time/residue: 0.2478 time to fit residues: 115.4147 Evaluate side-chains 241 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 248 GLN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN A1149 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13998 Z= 0.281 Angle : 0.559 8.139 18946 Z= 0.288 Chirality : 0.042 0.161 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.719 73.392 1966 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 11.64 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.21), residues: 1662 helix: 1.71 (0.17), residues: 956 sheet: -1.65 (0.52), residues: 72 loop : -0.80 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 480 HIS 0.018 0.001 HIS C 150 PHE 0.022 0.002 PHE A 629 TYR 0.020 0.002 TYR A1356 ARG 0.005 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 1.653 Fit side-chains REVERT: A 565 TYR cc_start: 0.8664 (t80) cc_final: 0.8288 (t80) REVERT: A 1308 PHE cc_start: 0.7658 (t80) cc_final: 0.7381 (t80) REVERT: B 152 LEU cc_start: 0.9104 (tp) cc_final: 0.8664 (tt) REVERT: C 140 GLU cc_start: 0.7616 (mp0) cc_final: 0.7014 (mp0) REVERT: D 131 ILE cc_start: 0.6269 (mp) cc_final: 0.5969 (mp) REVERT: E 195 MET cc_start: 0.7582 (mtp) cc_final: 0.7248 (mtt) outliers start: 31 outliers final: 18 residues processed: 262 average time/residue: 0.2455 time to fit residues: 97.2970 Evaluate side-chains 240 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 217 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13998 Z= 0.278 Angle : 0.538 7.883 18946 Z= 0.280 Chirality : 0.041 0.145 2201 Planarity : 0.004 0.044 2361 Dihedral : 7.643 73.411 1960 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.93 % Allowed : 15.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.21), residues: 1662 helix: 1.61 (0.17), residues: 965 sheet: -1.82 (0.55), residues: 61 loop : -0.92 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 932 HIS 0.014 0.001 HIS C 150 PHE 0.026 0.002 PHE A 87 TYR 0.012 0.001 TYR A1356 ARG 0.004 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 1.651 Fit side-chains REVERT: A 565 TYR cc_start: 0.8685 (t80) cc_final: 0.8248 (t80) REVERT: A 811 ASP cc_start: 0.8152 (p0) cc_final: 0.7939 (p0) REVERT: A 1308 PHE cc_start: 0.7684 (t80) cc_final: 0.7455 (t80) REVERT: B 152 LEU cc_start: 0.9106 (tp) cc_final: 0.8671 (tt) REVERT: C 140 GLU cc_start: 0.7667 (mp0) cc_final: 0.7084 (mp0) REVERT: D 131 ILE cc_start: 0.6250 (mp) cc_final: 0.5901 (mp) outliers start: 45 outliers final: 30 residues processed: 263 average time/residue: 0.2425 time to fit residues: 96.4316 Evaluate side-chains 253 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN C 128 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13998 Z= 0.227 Angle : 0.514 7.701 18946 Z= 0.267 Chirality : 0.040 0.153 2201 Planarity : 0.004 0.043 2361 Dihedral : 7.584 73.375 1960 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 18.27 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.21), residues: 1662 helix: 1.71 (0.16), residues: 952 sheet: -1.97 (0.52), residues: 69 loop : -0.81 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.020 0.001 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 565 TYR cc_start: 0.8724 (t80) cc_final: 0.8262 (t80) REVERT: A 1308 PHE cc_start: 0.7687 (t80) cc_final: 0.7475 (t80) REVERT: A 1372 LEU cc_start: 0.8328 (mt) cc_final: 0.8126 (mp) REVERT: B 152 LEU cc_start: 0.9117 (tp) cc_final: 0.8696 (tt) REVERT: C 140 GLU cc_start: 0.7693 (mp0) cc_final: 0.7116 (mp0) REVERT: D 131 ILE cc_start: 0.6269 (mp) cc_final: 0.5898 (mp) outliers start: 46 outliers final: 34 residues processed: 265 average time/residue: 0.2435 time to fit residues: 97.8711 Evaluate side-chains 264 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 229 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13998 Z= 0.294 Angle : 0.551 7.774 18946 Z= 0.284 Chirality : 0.041 0.165 2201 Planarity : 0.004 0.043 2361 Dihedral : 7.619 73.430 1960 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.71 % Allowed : 19.12 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.21), residues: 1662 helix: 1.62 (0.16), residues: 953 sheet: -2.00 (0.52), residues: 69 loop : -0.83 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.024 0.002 PHE A 87 TYR 0.012 0.001 TYR A 746 ARG 0.005 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 459 SER cc_start: 0.8926 (t) cc_final: 0.8589 (t) REVERT: A 483 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 565 TYR cc_start: 0.8742 (t80) cc_final: 0.8267 (t80) REVERT: A 811 ASP cc_start: 0.8176 (p0) cc_final: 0.7891 (p0) REVERT: A 875 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.6762 (p90) REVERT: A 1308 PHE cc_start: 0.7776 (t80) cc_final: 0.7547 (t80) REVERT: A 1372 LEU cc_start: 0.8356 (mt) cc_final: 0.8112 (mp) REVERT: B 152 LEU cc_start: 0.9117 (tp) cc_final: 0.8696 (tt) REVERT: B 175 GLU cc_start: 0.8448 (mp0) cc_final: 0.8027 (mt-10) REVERT: C 140 GLU cc_start: 0.7778 (mp0) cc_final: 0.7355 (mp0) REVERT: D 131 ILE cc_start: 0.6298 (mp) cc_final: 0.5877 (mp) outliers start: 57 outliers final: 39 residues processed: 264 average time/residue: 0.2459 time to fit residues: 98.2095 Evaluate side-chains 258 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 159 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13998 Z= 0.163 Angle : 0.495 7.178 18946 Z= 0.256 Chirality : 0.039 0.173 2201 Planarity : 0.003 0.048 2361 Dihedral : 7.485 73.373 1960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.06 % Allowed : 20.35 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.21), residues: 1662 helix: 1.81 (0.17), residues: 958 sheet: -1.79 (0.54), residues: 69 loop : -0.72 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.022 0.001 PHE A 87 TYR 0.012 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 321 LEU cc_start: 0.9325 (mt) cc_final: 0.9061 (mt) REVERT: A 340 MET cc_start: 0.8285 (tpt) cc_final: 0.8047 (tpt) REVERT: A 483 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 565 TYR cc_start: 0.8776 (t80) cc_final: 0.8272 (t80) REVERT: A 1422 MET cc_start: 0.7091 (ptt) cc_final: 0.6729 (ptt) REVERT: B 152 LEU cc_start: 0.9073 (tp) cc_final: 0.8654 (tt) REVERT: B 175 GLU cc_start: 0.8394 (mp0) cc_final: 0.8071 (mt-10) REVERT: C 140 GLU cc_start: 0.7736 (mp0) cc_final: 0.7382 (mp0) REVERT: D 131 ILE cc_start: 0.6320 (mp) cc_final: 0.5953 (mp) REVERT: D 132 THR cc_start: 0.6978 (m) cc_final: 0.6752 (m) outliers start: 47 outliers final: 33 residues processed: 280 average time/residue: 0.2541 time to fit residues: 107.8470 Evaluate side-chains 266 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13998 Z= 0.185 Angle : 0.510 7.631 18946 Z= 0.262 Chirality : 0.040 0.205 2201 Planarity : 0.003 0.049 2361 Dihedral : 7.475 73.342 1960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.38 % Allowed : 20.61 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.21), residues: 1662 helix: 1.82 (0.17), residues: 958 sheet: -1.85 (0.53), residues: 69 loop : -0.72 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.016 0.001 HIS C 150 PHE 0.021 0.001 PHE A 629 TYR 0.017 0.001 TYR A 34 ARG 0.007 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 234 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 376 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9154 (mm) REVERT: A 483 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7837 (pp) REVERT: A 565 TYR cc_start: 0.8788 (t80) cc_final: 0.8278 (t80) REVERT: A 811 ASP cc_start: 0.8099 (p0) cc_final: 0.7735 (p0) REVERT: A 875 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6246 (p90) REVERT: A 1422 MET cc_start: 0.7071 (ptt) cc_final: 0.6711 (ptt) REVERT: B 134 ARG cc_start: 0.7522 (ptm160) cc_final: 0.6951 (mtp-110) REVERT: B 152 LEU cc_start: 0.9054 (tp) cc_final: 0.8629 (tt) REVERT: B 175 GLU cc_start: 0.8385 (mp0) cc_final: 0.8112 (mt-10) REVERT: D 131 ILE cc_start: 0.6340 (mp) cc_final: 0.5957 (mp) outliers start: 52 outliers final: 43 residues processed: 268 average time/residue: 0.2515 time to fit residues: 102.1965 Evaluate side-chains 273 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13998 Z= 0.143 Angle : 0.510 8.928 18946 Z= 0.260 Chirality : 0.039 0.192 2201 Planarity : 0.003 0.050 2361 Dihedral : 7.388 73.386 1960 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.19 % Allowed : 21.52 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.21), residues: 1662 helix: 1.91 (0.17), residues: 958 sheet: -1.79 (0.54), residues: 69 loop : -0.64 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 203 HIS 0.015 0.001 HIS C 150 PHE 0.024 0.001 PHE A 87 TYR 0.013 0.001 TYR A 746 ARG 0.008 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 459 SER cc_start: 0.8869 (t) cc_final: 0.8539 (t) REVERT: A 483 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7799 (pp) REVERT: A 565 TYR cc_start: 0.8760 (t80) cc_final: 0.8237 (t80) REVERT: A 811 ASP cc_start: 0.8002 (p0) cc_final: 0.7690 (p0) REVERT: A 875 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6049 (p90) REVERT: A 954 ASP cc_start: 0.8019 (m-30) cc_final: 0.7709 (m-30) REVERT: A 1037 ASN cc_start: 0.8373 (m-40) cc_final: 0.8067 (m-40) REVERT: B 134 ARG cc_start: 0.7409 (ptm160) cc_final: 0.6663 (mtp-110) REVERT: C 177 MET cc_start: 0.8263 (tpp) cc_final: 0.7991 (tpp) REVERT: D 131 ILE cc_start: 0.6315 (mp) cc_final: 0.5931 (mp) REVERT: D 132 THR cc_start: 0.6935 (m) cc_final: 0.6700 (m) outliers start: 49 outliers final: 32 residues processed: 282 average time/residue: 0.2519 time to fit residues: 107.1503 Evaluate side-chains 273 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13998 Z= 0.270 Angle : 0.574 13.419 18946 Z= 0.293 Chirality : 0.042 0.204 2201 Planarity : 0.004 0.044 2361 Dihedral : 7.529 73.416 1960 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.71 % Allowed : 21.59 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.21), residues: 1662 helix: 1.68 (0.17), residues: 956 sheet: -1.84 (0.53), residues: 69 loop : -0.73 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 203 HIS 0.016 0.001 HIS C 150 PHE 0.020 0.002 PHE A 629 TYR 0.019 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8396 (mp) REVERT: A 376 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9159 (mm) REVERT: A 459 SER cc_start: 0.8948 (t) cc_final: 0.8631 (t) REVERT: A 483 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7828 (pp) REVERT: A 565 TYR cc_start: 0.8794 (t80) cc_final: 0.8284 (t80) REVERT: A 875 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6107 (p90) REVERT: B 134 ARG cc_start: 0.7438 (ptm160) cc_final: 0.6843 (mtp-110) REVERT: D 131 ILE cc_start: 0.6325 (mp) cc_final: 0.5890 (mp) outliers start: 57 outliers final: 41 residues processed: 262 average time/residue: 0.2596 time to fit residues: 103.7104 Evaluate side-chains 264 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 219 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13998 Z= 0.328 Angle : 0.614 15.239 18946 Z= 0.313 Chirality : 0.043 0.193 2201 Planarity : 0.004 0.039 2361 Dihedral : 7.666 73.470 1960 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.38 % Allowed : 21.98 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.21), residues: 1662 helix: 1.48 (0.16), residues: 956 sheet: -1.96 (0.52), residues: 69 loop : -0.85 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.022 0.002 PHE A 629 TYR 0.020 0.002 TYR A 746 ARG 0.009 0.000 ARG C 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 1.708 Fit side-chains REVERT: A 131 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 459 SER cc_start: 0.9009 (t) cc_final: 0.8712 (t) REVERT: A 483 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 565 TYR cc_start: 0.8826 (t80) cc_final: 0.8334 (t80) REVERT: A 586 TYR cc_start: 0.7856 (m-80) cc_final: 0.7472 (m-10) REVERT: A 875 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6022 (p90) REVERT: A 1168 MET cc_start: 0.7475 (ttm) cc_final: 0.7243 (ttp) REVERT: D 131 ILE cc_start: 0.6357 (mp) cc_final: 0.5920 (mp) REVERT: E 177 MET cc_start: 0.8158 (mtp) cc_final: 0.7868 (mtp) outliers start: 52 outliers final: 44 residues processed: 261 average time/residue: 0.2669 time to fit residues: 106.0134 Evaluate side-chains 264 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 134 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099358 restraints weight = 24995.508| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.10 r_work: 0.3069 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13998 Z= 0.202 Angle : 0.580 15.540 18946 Z= 0.295 Chirality : 0.041 0.273 2201 Planarity : 0.004 0.040 2361 Dihedral : 7.594 73.343 1960 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.99 % Allowed : 22.24 % Favored : 74.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.21), residues: 1662 helix: 1.61 (0.17), residues: 957 sheet: -1.86 (0.53), residues: 69 loop : -0.75 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.029 0.001 PHE A 629 TYR 0.022 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3145.09 seconds wall clock time: 58 minutes 34.09 seconds (3514.09 seconds total)