Starting phenix.real_space_refine on Wed Aug 5 21:30:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja3_61289/08_2026/9ja3_61289.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.021 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 50 5.49 5 S 46 5.16 5 C 7182 2.51 5 N 2017 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11493 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8444 Classifications: {'peptide': 1085} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2058 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain breaks: 1 Chain: "T" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 418 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'AVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.19 Number of scatterers: 11493 At special positions: 0 Unit cell: (82.32, 114.24, 153.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 46 16.00 P 50 15.00 O 2195 8.00 N 2017 7.00 C 7182 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 - 3.00 Amino acid : True - 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: 0.58 Conformation dependent library (CDL) restraints added in 401.3 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 37.9% alpha, 18.0% beta 13 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.638A pdb=" N ARG A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.079A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.759A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.655A pdb=" N SER A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.757A pdb=" N ASN A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.543A pdb=" N ARG A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.588A pdb=" N MET A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.710A pdb=" N ILE A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.501A pdb=" N ASP A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.663A pdb=" N GLY A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 removed outlier: 4.211A pdb=" N GLU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 3.537A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 628 " --> pdb=" O CYS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 772 through 790 removed outlier: 4.183A pdb=" N ILE A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 783 " --> pdb=" O ARG A 779 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 785 " --> pdb=" O TRP A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 822 removed outlier: 3.714A pdb=" N LYS A 805 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 4.009A pdb=" N ALA A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 898 through 902 removed outlier: 3.613A pdb=" N GLY A 901 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 902 " --> pdb=" O ALA A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 898 through 902' Processing helix chain 'A' and resid 903 through 918 Processing helix chain 'A' and resid 955 through 959 Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 980 through 991 removed outlier: 3.761A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 removed outlier: 3.575A pdb=" N TRP A 998 " --> pdb=" O PRO A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1022 Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 4.170A pdb=" N VAL A1032 " --> pdb=" O GLN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1044 Processing helix chain 'A' and resid 1051 through 1061 Processing helix chain 'A' and resid 1080 through 1095 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1157 through 1174 Processing helix chain 'A' and resid 1175 through 1178 removed outlier: 3.754A pdb=" N GLY A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1192 removed outlier: 3.545A pdb=" N PHE A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A1192 " --> pdb=" O LEU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1209 Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 3.655A pdb=" N ARG A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 removed outlier: 4.126A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 107 through 112 removed outlier: 4.315A pdb=" N VAL B 111 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 275 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.368A pdb=" N ARG A 193 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N PHE A 343 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 195 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N CYS A 345 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A 197 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 187 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 149 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.514A pdb=" N GLN A 203 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 635 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 256 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.586A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 393 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS A 363 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR A 463 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N MET A 365 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 464 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 709 removed outlier: 5.284A pdb=" N CYS A 926 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A 717 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 707 through 709 removed outlier: 6.855A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 935 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS A 940 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 752 through 757 Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id=AB3, first strand: chain 'A' and resid 1211 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AB6, first strand: chain 'B' and resid 177 through 178 449 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3349 1.34 - 1.45: 2051 1.45 - 1.57: 6279 1.57 - 1.69: 97 1.69 - 1.81: 68 Bond restraints: 11844 Sorted by residual: bond pdb=" O3B AVP T 101 " pdb=" PG AVP T 101 " ideal model delta sigma weight residual 1.740 1.600 0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C5 AVP T 101 " pdb=" C6 AVP T 101 " ideal model delta sigma weight residual 1.424 1.330 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3A AVP T 101 " pdb=" PB AVP T 101 " ideal model delta sigma weight residual 1.671 1.608 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O3G AVP T 101 " pdb=" PG AVP T 101 " ideal model delta sigma weight residual 1.522 1.467 0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" O2G AVP T 101 " pdb=" PG AVP T 101 " ideal model delta sigma weight residual 1.524 1.469 0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 11839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 15989 1.85 - 3.70: 270 3.70 - 5.55: 21 5.55 - 7.40: 4 7.40 - 9.25: 6 Bond angle restraints: 16290 Sorted by residual: angle pdb=" O4' DG T 5 " pdb=" C4' DG T 5 " pdb=" C3' DG T 5 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.01e+01 angle pdb=" N3 DT P -15 " pdb=" C4 DT P -15 " pdb=" O4 DT P -15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT P -7 " pdb=" C4 DT P -7 " pdb=" O4 DT P -7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T -11 " pdb=" C4 DT T -11 " pdb=" O4 DT T -11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 16285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.61: 6489 29.61 - 59.22: 400 59.22 - 88.82: 32 88.82 - 118.43: 0 118.43 - 148.04: 2 Dihedral angle restraints: 6923 sinusoidal: 3013 harmonic: 3910 Sorted by residual: dihedral pdb=" C4' DG T 10 " pdb=" C3' DG T 10 " pdb=" O3' DG T 10 " pdb=" P DC T 11 " ideal model delta sinusoidal sigma weight residual 220.00 71.96 148.04 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" C4' DG P -12 " pdb=" C3' DG P -12 " pdb=" O3' DG P -12 " pdb=" P DA P -11 " ideal model delta sinusoidal sigma weight residual 220.00 85.14 134.86 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA ILE A 613 " pdb=" C ILE A 613 " pdb=" N TYR A 614 " pdb=" CA TYR A 614 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 6920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1415 0.045 - 0.091: 325 0.091 - 0.136: 98 0.136 - 0.181: 3 0.181 - 0.226: 3 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CB THR A 735 " pdb=" CA THR A 735 " pdb=" OG1 THR A 735 " pdb=" CG2 THR A 735 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' DG T 10 " pdb=" C4' DG T 10 " pdb=" O3' DG T 10 " pdb=" C2' DG T 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1841 not shown) Planarity restraints: 1936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 88 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG B 88 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG B 88 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 291 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C PHE B 291 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE B 291 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 292 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 87 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A 88 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " -0.023 5.00e-02 4.00e+02 ... (remaining 1933 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1788 2.76 - 3.30: 10468 3.30 - 3.83: 19073 3.83 - 4.37: 22004 4.37 - 4.90: 37912 Nonbonded interactions: 91245 Sorted by model distance: nonbonded pdb=" OG SER B 57 " pdb=" O HIS B 69 " model vdw 2.229 3.040 nonbonded pdb=" O2 DC T 12 " pdb=" N2 DG P -19 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A1044 " pdb=" OP1 DC P -3 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 465 " pdb=" O TYR A 538 " model vdw 2.291 3.040 nonbonded pdb=" NZ LYS B 289 " pdb=" OG1 THR B 302 " model vdw 2.311 3.120 ... (remaining 91240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 0.140 11844 Z= 0.246 Angle : 0.556 9.246 16290 Z= 0.361 Chirality : 0.042 0.226 1844 Planarity : 0.003 0.041 1936 Dihedral : 17.368 148.040 4409 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.89 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1342 helix: 1.68 (0.27), residues: 422 sheet: -0.16 (0.34), residues: 244 loop : -1.32 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.014 0.001 TYR A 399 PHE 0.009 0.001 PHE A 367 TRP 0.007 0.001 TRP A 502 HIS 0.005 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.25 (11844) covalent geometry : angle 0.55637 / 0.36 (16290) hydrogen bonds : bond 0.17370 / 11.52 ( 476) hydrogen bonds : angle 7.06444 / 4.90 ( 1301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.7035 (mt) cc_final: 0.6723 (mt) REVERT: A 787 GLN cc_start: 0.7455 (tp40) cc_final: 0.7217 (tp40) REVERT: A 1229 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7840 (tmt170) REVERT: B 202 PHE cc_start: 0.6449 (m-80) cc_final: 0.6013 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0990 time to fit residues: 23.2202 Evaluate side-chains 116 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 423 HIS A1179 ASN B 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.174646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124770 restraints weight = 15549.114| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.55 r_work: 0.3449 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11844 Z= 0.171 Angle : 0.592 6.603 16290 Z= 0.319 Chirality : 0.046 0.356 1844 Planarity : 0.004 0.068 1936 Dihedral : 17.648 151.656 2015 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 1.46 % Allowed : 7.76 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1342 helix: 1.35 (0.26), residues: 442 sheet: -0.00 (0.33), residues: 239 loop : -1.45 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.019 0.002 TYR A 399 PHE 0.018 0.001 PHE A1162 TRP 0.005 0.001 TRP B 141 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (11844) covalent geometry : angle 0.59225 / 0.32 (16290) hydrogen bonds : bond 0.05869 / 4.07 ( 476) hydrogen bonds : angle 5.12427 / 3.62 ( 1301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 782 LEU cc_start: 0.8220 (mt) cc_final: 0.8000 (mp) REVERT: A 787 GLN cc_start: 0.7469 (tp40) cc_final: 0.7154 (tp40) REVERT: A 1226 MET cc_start: 0.6241 (tpt) cc_final: 0.6023 (tpt) REVERT: A 1229 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7582 (ttt-90) REVERT: B 158 MET cc_start: 0.7336 (mtm) cc_final: 0.7124 (mtt) REVERT: B 202 PHE cc_start: 0.6533 (m-80) cc_final: 0.6206 (m-80) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.0991 time to fit residues: 17.3619 Evaluate side-chains 116 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 423 HIS ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.167141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118062 restraints weight = 15948.686| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.75 r_work: 0.3331 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11844 Z= 0.251 Angle : 0.685 7.969 16290 Z= 0.362 Chirality : 0.048 0.349 1844 Planarity : 0.005 0.076 1936 Dihedral : 18.237 152.935 2015 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer: Outliers : 2.19 % Allowed : 10.86 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1342 helix: 0.85 (0.25), residues: 436 sheet: -0.40 (0.33), residues: 240 loop : -1.70 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 492 TYR 0.023 0.002 TYR A 399 PHE 0.029 0.002 PHE A 590 TRP 0.011 0.002 TRP A1196 HIS 0.012 0.002 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (11844) covalent geometry : angle 0.68486 / 0.36 (16290) hydrogen bonds : bond 0.06040 / 4.16 ( 476) hydrogen bonds : angle 5.34745 / 3.76 ( 1301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7014 (m) REVERT: A 511 LYS cc_start: 0.8015 (ptpt) cc_final: 0.7661 (ptpt) REVERT: A 782 LEU cc_start: 0.8426 (mt) cc_final: 0.8216 (mp) REVERT: A 1079 GLN cc_start: 0.7934 (tt0) cc_final: 0.7638 (tp40) REVERT: A 1138 LEU cc_start: 0.7592 (mt) cc_final: 0.7204 (mm) REVERT: A 1229 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7641 (ttt-90) REVERT: B 72 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6662 (mm) REVERT: B 158 MET cc_start: 0.7496 (mtm) cc_final: 0.7257 (mtt) REVERT: B 202 PHE cc_start: 0.6570 (m-80) cc_final: 0.6230 (m-80) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 0.0806 time to fit residues: 16.4736 Evaluate side-chains 128 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.169594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119805 restraints weight = 15738.461| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.65 r_work: 0.3370 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11844 Z= 0.141 Angle : 0.584 6.469 16290 Z= 0.312 Chirality : 0.044 0.358 1844 Planarity : 0.004 0.075 1936 Dihedral : 18.217 150.185 2015 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.56 % Favored : 93.22 % Rotamer: Outliers : 1.82 % Allowed : 12.50 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1342 helix: 0.87 (0.25), residues: 451 sheet: -0.44 (0.33), residues: 240 loop : -1.64 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.020 0.001 TYR A 878 PHE 0.021 0.001 PHE A 499 TRP 0.007 0.001 TRP B 141 HIS 0.006 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11844) covalent geometry : angle 0.58440 / 0.31 (16290) hydrogen bonds : bond 0.04899 / 3.42 ( 476) hydrogen bonds : angle 5.05063 / 3.54 ( 1301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.7143 (m) REVERT: A 1079 GLN cc_start: 0.7941 (tt0) cc_final: 0.7628 (tp40) REVERT: A 1138 LEU cc_start: 0.7643 (mt) cc_final: 0.7227 (mm) REVERT: A 1166 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 72 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6536 (mm) REVERT: B 158 MET cc_start: 0.7498 (mtm) cc_final: 0.7255 (mtt) REVERT: B 202 PHE cc_start: 0.6646 (m-80) cc_final: 0.6239 (m-80) outliers start: 20 outliers final: 11 residues processed: 132 average time/residue: 0.0777 time to fit residues: 15.3278 Evaluate side-chains 126 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.167423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119080 restraints weight = 15621.797| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.78 r_work: 0.3346 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11844 Z= 0.183 Angle : 0.611 7.849 16290 Z= 0.323 Chirality : 0.045 0.359 1844 Planarity : 0.005 0.079 1936 Dihedral : 18.149 149.446 2015 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.97 % Favored : 91.80 % Rotamer: Outliers : 2.74 % Allowed : 12.96 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1342 helix: 0.91 (0.25), residues: 445 sheet: -0.57 (0.33), residues: 242 loop : -1.72 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.019 0.002 TYR A 399 PHE 0.020 0.001 PHE A 499 TRP 0.008 0.001 TRP A1196 HIS 0.007 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (11844) covalent geometry : angle 0.61149 / 0.32 (16290) hydrogen bonds : bond 0.05068 / 3.52 ( 476) hydrogen bonds : angle 5.03299 / 3.52 ( 1301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: A 176 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7351 (m) REVERT: A 540 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 799 GLU cc_start: 0.6462 (tp30) cc_final: 0.6225 (tp30) REVERT: A 827 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 1079 GLN cc_start: 0.7962 (tt0) cc_final: 0.7615 (tp40) REVERT: A 1138 LEU cc_start: 0.7654 (mt) cc_final: 0.7245 (mm) REVERT: A 1166 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 158 MET cc_start: 0.7475 (mtm) cc_final: 0.7217 (mtt) REVERT: B 202 PHE cc_start: 0.6651 (m-80) cc_final: 0.6372 (m-80) outliers start: 30 outliers final: 17 residues processed: 140 average time/residue: 0.0816 time to fit residues: 16.9676 Evaluate side-chains 138 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 115 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122392 restraints weight = 15579.350| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.93 r_work: 0.3364 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11844 Z= 0.126 Angle : 0.591 17.633 16290 Z= 0.308 Chirality : 0.043 0.364 1844 Planarity : 0.004 0.082 1936 Dihedral : 18.053 147.698 2015 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 2.46 % Allowed : 13.32 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1342 helix: 1.01 (0.25), residues: 451 sheet: -0.41 (0.33), residues: 240 loop : -1.58 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.018 0.001 TYR A 399 PHE 0.019 0.001 PHE A 499 TRP 0.008 0.001 TRP A1196 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (11844) covalent geometry : angle 0.59132 / 0.31 (16290) hydrogen bonds : bond 0.04397 / 3.06 ( 476) hydrogen bonds : angle 4.84775 / 3.38 ( 1301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: A 176 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7340 (m) REVERT: A 827 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7572 (pp) REVERT: A 1007 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 1079 GLN cc_start: 0.7865 (tt0) cc_final: 0.7527 (tp40) REVERT: A 1138 LEU cc_start: 0.7623 (mt) cc_final: 0.7248 (mm) REVERT: A 1166 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 72 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6541 (mm) REVERT: B 158 MET cc_start: 0.7179 (mtm) cc_final: 0.6912 (mtt) REVERT: B 202 PHE cc_start: 0.6725 (m-80) cc_final: 0.6270 (m-80) outliers start: 27 outliers final: 19 residues processed: 142 average time/residue: 0.0834 time to fit residues: 17.2498 Evaluate side-chains 142 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 125 optimal weight: 0.0670 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.170514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122242 restraints weight = 15494.797| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.46 r_work: 0.3398 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11844 Z= 0.118 Angle : 0.572 13.527 16290 Z= 0.299 Chirality : 0.043 0.366 1844 Planarity : 0.004 0.079 1936 Dihedral : 17.917 146.266 2015 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.86 % Favored : 92.92 % Rotamer: Outliers : 2.55 % Allowed : 14.14 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.24), residues: 1342 helix: 1.23 (0.26), residues: 445 sheet: -0.60 (0.32), residues: 248 loop : -1.51 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1048 TYR 0.017 0.001 TYR A 399 PHE 0.020 0.001 PHE A 499 TRP 0.005 0.001 TRP A1196 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (11844) covalent geometry : angle 0.57201 / 0.30 (16290) hydrogen bonds : bond 0.04108 / 2.85 ( 476) hydrogen bonds : angle 4.70406 / 3.27 ( 1301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: A 176 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7347 (m) REVERT: A 787 GLN cc_start: 0.7583 (tp40) cc_final: 0.7352 (tp40) REVERT: A 827 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7552 (pp) REVERT: A 1007 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 1079 GLN cc_start: 0.7952 (tt0) cc_final: 0.7610 (tp40) REVERT: A 1138 LEU cc_start: 0.7573 (mt) cc_final: 0.7185 (mm) REVERT: B 202 PHE cc_start: 0.6649 (m-80) cc_final: 0.6272 (m-80) outliers start: 28 outliers final: 16 residues processed: 141 average time/residue: 0.0770 time to fit residues: 16.0349 Evaluate side-chains 135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 115 optimal weight: 0.2980 chunk 127 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.170338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120015 restraints weight = 15664.590| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.52 r_work: 0.3388 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11844 Z= 0.129 Angle : 0.578 13.482 16290 Z= 0.301 Chirality : 0.043 0.369 1844 Planarity : 0.004 0.082 1936 Dihedral : 17.888 145.578 2015 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 2.19 % Allowed : 15.24 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1342 helix: 1.12 (0.25), residues: 451 sheet: -0.60 (0.32), residues: 253 loop : -1.50 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.015 0.001 TYR A 399 PHE 0.017 0.001 PHE A 499 TRP 0.006 0.001 TRP A1196 HIS 0.005 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11844) covalent geometry : angle 0.57789 / 0.30 (16290) hydrogen bonds : bond 0.04167 / 2.88 ( 476) hydrogen bonds : angle 4.69730 / 3.26 ( 1301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: A 176 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7348 (m) REVERT: A 333 MET cc_start: 0.8664 (tpt) cc_final: 0.8441 (tpt) REVERT: A 787 GLN cc_start: 0.7562 (tp40) cc_final: 0.7304 (tp40) REVERT: A 827 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7524 (pp) REVERT: A 1007 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7838 (mp) REVERT: A 1079 GLN cc_start: 0.7948 (tt0) cc_final: 0.7569 (tp40) REVERT: A 1138 LEU cc_start: 0.7552 (mt) cc_final: 0.7142 (mm) REVERT: A 1166 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 202 PHE cc_start: 0.6592 (m-80) cc_final: 0.6216 (m-80) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.0840 time to fit residues: 16.6253 Evaluate side-chains 134 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.169103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118926 restraints weight = 15581.733| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.64 r_work: 0.3360 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11844 Z= 0.146 Angle : 0.592 12.119 16290 Z= 0.309 Chirality : 0.044 0.369 1844 Planarity : 0.005 0.083 1936 Dihedral : 17.861 144.683 2015 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.38 % Favored : 92.47 % Rotamer: Outliers : 2.19 % Allowed : 15.33 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1342 helix: 1.19 (0.25), residues: 445 sheet: -0.70 (0.32), residues: 255 loop : -1.52 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.018 0.001 TYR A 399 PHE 0.018 0.001 PHE A 499 TRP 0.011 0.001 TRP A1196 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11844) covalent geometry : angle 0.59220 / 0.31 (16290) hydrogen bonds : bond 0.04356 / 3.02 ( 476) hydrogen bonds : angle 4.74344 / 3.30 ( 1301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: A 787 GLN cc_start: 0.7478 (tp40) cc_final: 0.7199 (tp40) REVERT: A 827 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7573 (pp) REVERT: A 1007 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 1079 GLN cc_start: 0.7885 (tt0) cc_final: 0.7521 (tp40) REVERT: A 1138 LEU cc_start: 0.7542 (mt) cc_final: 0.7165 (mm) REVERT: A 1166 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7871 (mp) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.0888 time to fit residues: 17.7750 Evaluate side-chains 138 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121247 restraints weight = 15665.223| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.51 r_work: 0.3402 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11844 Z= 0.110 Angle : 0.568 12.526 16290 Z= 0.298 Chirality : 0.042 0.371 1844 Planarity : 0.004 0.082 1936 Dihedral : 17.701 143.344 2015 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 1.64 % Allowed : 16.15 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1342 helix: 1.26 (0.26), residues: 449 sheet: -0.59 (0.32), residues: 253 loop : -1.50 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.015 0.001 TYR A 399 PHE 0.017 0.001 PHE A 499 TRP 0.005 0.001 TRP A1196 HIS 0.006 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (11844) covalent geometry : angle 0.56841 / 0.30 (16290) hydrogen bonds : bond 0.03879 / 2.69 ( 476) hydrogen bonds : angle 4.60401 / 3.20 ( 1301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: A 787 GLN cc_start: 0.7548 (tp40) cc_final: 0.7277 (tp40) REVERT: A 827 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7390 (pp) REVERT: A 1007 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 1079 GLN cc_start: 0.7941 (tt0) cc_final: 0.7562 (tp40) REVERT: A 1138 LEU cc_start: 0.7543 (mt) cc_final: 0.7152 (mm) REVERT: A 1166 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7788 (mp) REVERT: B 76 GLN cc_start: 0.8136 (mm110) cc_final: 0.7903 (mm-40) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1026 time to fit residues: 19.9196 Evaluate side-chains 131 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121376 restraints weight = 15703.641| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.62 r_work: 0.3398 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11844 Z= 0.117 Angle : 0.567 11.975 16290 Z= 0.296 Chirality : 0.042 0.372 1844 Planarity : 0.004 0.083 1936 Dihedral : 17.636 142.695 2015 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 1.92 % Allowed : 15.97 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1342 helix: 1.37 (0.26), residues: 445 sheet: -0.55 (0.32), residues: 253 loop : -1.50 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.015 0.001 TYR A 399 PHE 0.017 0.001 PHE A 499 TRP 0.007 0.001 TRP A1196 HIS 0.005 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (11844) covalent geometry : angle 0.56728 / 0.30 (16290) hydrogen bonds : bond 0.03868 / 2.68 ( 476) hydrogen bonds : angle 4.58441 / 3.20 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.89 seconds wall clock time: 46 minutes 41.59 seconds (2801.59 seconds total)