Starting phenix.real_space_refine on Fri Jul 3 03:28:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja3_61289/07_2026/9ja3_61289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja3_61289/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja3_61289/07_2026/9ja3_61289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja3_61289/07_2026/9ja3_61289.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja3_61289/07_2026/9ja3_61289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja3_61289/07_2026/9ja3_61289.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 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: 0.64 Conformation dependent library (CDL) restraints added in 360.3 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: 1.48 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: 2.17 Time building geometry restraints manager: 0.83 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: 15990 1.85 - 3.70: 270 3.70 - 5.55: 20 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: 4.100 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.880 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: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- 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 : 0.555 9.246 16290 Z= 0.359 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 0.55494 / 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 : 0.394 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: 0.6014 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1021 time to fit residues: 23.9225 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 : 0.411 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124292 restraints weight = 15564.412| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.49 r_work: 0.3444 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11844 Z= 0.176 Angle : 0.613 6.728 16290 Z= 0.329 Chirality : 0.046 0.331 1844 Planarity : 0.005 0.063 1936 Dihedral : 17.668 153.721 2015 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 1.28 % Allowed : 7.76 % Favored : 90.97 % 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: -0.38 (0.24), residues: 1342 helix: 1.31 (0.26), residues: 441 sheet: -0.04 (0.33), residues: 239 loop : -1.45 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.020 0.002 TYR A 399 PHE 0.019 0.001 PHE A1162 TRP 0.006 0.001 TRP B 141 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (11844) covalent geometry : angle 0.61263 / 0.33 (16290) hydrogen bonds : bond 0.05663 / 3.94 ( 476) hydrogen bonds : angle 5.09679 / 3.60 ( 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 139 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 787 GLN cc_start: 0.7493 (tp40) cc_final: 0.7179 (tp40) REVERT: A 888 ASP cc_start: 0.8034 (p0) cc_final: 0.7784 (p0) REVERT: A 1226 MET cc_start: 0.6225 (tpt) cc_final: 0.5998 (tpt) REVERT: A 1229 ARG cc_start: 0.7962 (ttt-90) cc_final: 0.7690 (ttt-90) REVERT: B 202 PHE cc_start: 0.6534 (m-80) cc_final: 0.6222 (m-80) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 0.1045 time to fit residues: 18.8535 Evaluate side-chains 116 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 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: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS ** A 494 ASN ** 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 = 0.4093 r_free = 0.4093 target = 0.166394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118913 restraints weight = 16008.590| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.24 r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11844 Z= 0.283 Angle : 0.715 9.323 16290 Z= 0.376 Chirality : 0.049 0.314 1844 Planarity : 0.005 0.078 1936 Dihedral : 18.314 154.518 2015 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 2.10 % Allowed : 11.41 % Favored : 86.50 % 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: -0.99 (0.23), residues: 1342 helix: 0.75 (0.25), residues: 436 sheet: -0.48 (0.33), residues: 241 loop : -1.72 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 492 TYR 0.023 0.003 TYR A 399 PHE 0.029 0.002 PHE A 590 TRP 0.012 0.002 TRP A1196 HIS 0.011 0.002 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.28 (11844) covalent geometry : angle 0.71467 / 0.38 (16290) hydrogen bonds : bond 0.06316 / 4.34 ( 476) hydrogen bonds : angle 5.41610 / 3.82 ( 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 146 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7107 (m) REVERT: A 511 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7671 (ptpt) REVERT: A 1079 GLN cc_start: 0.7924 (tt0) cc_final: 0.7655 (tp40) REVERT: A 1138 LEU cc_start: 0.7657 (mt) cc_final: 0.7272 (mm) REVERT: A 1229 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7591 (ttt-90) REVERT: B 70 ASN cc_start: 0.8076 (t0) cc_final: 0.7211 (t0) REVERT: B 72 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6644 (mm) REVERT: B 202 PHE cc_start: 0.6559 (m-80) cc_final: 0.6217 (m-80) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.0965 time to fit residues: 19.3468 Evaluate side-chains 126 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 547 VAL 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 B residue 72 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: 0.9990 chunk 68 optimal weight: 0.2980 chunk 41 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.170593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121777 restraints weight = 15757.863| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.93 r_work: 0.3373 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2027 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= 0.123 Angle : 0.575 6.544 16290 Z= 0.307 Chirality : 0.044 0.328 1844 Planarity : 0.004 0.076 1936 Dihedral : 18.203 151.005 2015 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % 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: -0.77 (0.23), residues: 1342 helix: 0.90 (0.25), residues: 450 sheet: -0.43 (0.33), residues: 240 loop : -1.59 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 512 TYR 0.019 0.001 TYR A 399 PHE 0.018 0.001 PHE A 499 TRP 0.008 0.001 TRP B 141 HIS 0.006 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11844) covalent geometry : angle 0.57522 / 0.31 (16290) hydrogen bonds : bond 0.04733 / 3.31 ( 476) hydrogen bonds : angle 5.02151 / 3.52 ( 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 142 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7028 (m) REVERT: A 1079 GLN cc_start: 0.7819 (tt0) cc_final: 0.7517 (tp40) REVERT: A 1138 LEU cc_start: 0.7562 (mt) cc_final: 0.7184 (mm) REVERT: A 1166 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 70 ASN cc_start: 0.7755 (t0) cc_final: 0.6950 (t0) REVERT: B 72 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6372 (mm) REVERT: B 202 PHE cc_start: 0.6730 (m-80) cc_final: 0.6316 (m-80) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.0783 time to fit residues: 15.7733 Evaluate side-chains 124 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 541 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 777 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 A residue 1221 GLU Chi-restraints excluded: chain B residue 72 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: 0.9980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.170056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121639 restraints weight = 15564.904| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.90 r_work: 0.3370 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11844 Z= 0.132 Angle : 0.567 6.265 16290 Z= 0.301 Chirality : 0.043 0.329 1844 Planarity : 0.004 0.077 1936 Dihedral : 17.968 149.838 2015 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.00 % Favored : 92.77 % Rotamer: Outliers : 1.73 % Allowed : 13.41 % Favored : 84.85 % 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: -0.70 (0.23), residues: 1342 helix: 1.08 (0.25), residues: 444 sheet: -0.44 (0.33), residues: 240 loop : -1.60 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.018 0.001 TYR A 399 PHE 0.016 0.001 PHE A 499 TRP 0.007 0.001 TRP B 141 HIS 0.005 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11844) covalent geometry : angle 0.56745 / 0.30 (16290) hydrogen bonds : bond 0.04540 / 3.16 ( 476) hydrogen bonds : angle 4.88806 / 3.42 ( 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 139 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7111 (m) REVERT: A 827 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (pp) REVERT: A 1079 GLN cc_start: 0.7818 (tt0) cc_final: 0.7512 (tp40) REVERT: A 1138 LEU cc_start: 0.7518 (mt) cc_final: 0.7157 (mm) REVERT: B 70 ASN cc_start: 0.7879 (t0) cc_final: 0.6950 (t0) REVERT: B 72 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6274 (mm) REVERT: B 202 PHE cc_start: 0.6683 (m-80) cc_final: 0.6365 (m-80) outliers start: 19 outliers final: 11 residues processed: 135 average time/residue: 0.0893 time to fit residues: 17.7649 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 : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 735 THR 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 B residue 72 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: 0.8980 chunk 65 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.170603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121062 restraints weight = 15565.478| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.51 r_work: 0.3395 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2201 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= 0.123 Angle : 0.580 17.923 16290 Z= 0.302 Chirality : 0.043 0.333 1844 Planarity : 0.004 0.081 1936 Dihedral : 17.908 148.325 2015 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 1.73 % Allowed : 13.96 % 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: -0.67 (0.24), residues: 1342 helix: 1.09 (0.25), residues: 450 sheet: -0.62 (0.32), residues: 250 loop : -1.50 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.017 0.001 TYR A 399 PHE 0.017 0.001 PHE A 499 TRP 0.008 0.001 TRP A1196 HIS 0.005 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11844) covalent geometry : angle 0.58042 / 0.30 (16290) hydrogen bonds : bond 0.04271 / 2.96 ( 476) hydrogen bonds : angle 4.78773 / 3.35 ( 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 139 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7209 (m) REVERT: A 557 TYR cc_start: 0.7304 (p90) cc_final: 0.7096 (p90) REVERT: A 827 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7500 (pp) REVERT: A 888 ASP cc_start: 0.8340 (p0) cc_final: 0.8095 (p0) REVERT: A 1007 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 1079 GLN cc_start: 0.7951 (tt0) cc_final: 0.7587 (tp40) REVERT: A 1138 LEU cc_start: 0.7546 (mt) cc_final: 0.7155 (mm) REVERT: A 1166 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 70 ASN cc_start: 0.7896 (t0) cc_final: 0.6988 (t0) REVERT: B 72 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6487 (mm) REVERT: B 202 PHE cc_start: 0.6724 (m-80) cc_final: 0.6279 (m-80) outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 0.0867 time to fit residues: 17.7210 Evaluate side-chains 129 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1166 LEU Chi-restraints excluded: chain B residue 72 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: 1.9990 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 ASN B 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.168198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120329 restraints weight = 15666.348| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.38 r_work: 0.3353 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11844 Z= 0.177 Angle : 0.619 13.090 16290 Z= 0.323 Chirality : 0.044 0.332 1844 Planarity : 0.005 0.080 1936 Dihedral : 17.872 148.627 2015 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer: Outliers : 2.83 % Allowed : 13.69 % Favored : 83.49 % 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: -0.76 (0.23), residues: 1342 helix: 1.05 (0.25), residues: 444 sheet: -0.55 (0.33), residues: 247 loop : -1.62 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.019 0.002 TYR A 399 PHE 0.019 0.001 PHE A 590 TRP 0.011 0.001 TRP A1196 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11844) covalent geometry : angle 0.61921 / 0.32 (16290) hydrogen bonds : bond 0.04806 / 3.32 ( 476) hydrogen bonds : angle 4.89476 / 3.41 ( 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: 31 poor density : 116 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7363 (m) REVERT: A 540 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7830 (tp) REVERT: A 827 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7757 (pp) REVERT: A 1007 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 1079 GLN cc_start: 0.7994 (tt0) cc_final: 0.7626 (tp40) REVERT: A 1138 LEU cc_start: 0.7691 (mt) cc_final: 0.7266 (mm) REVERT: A 1166 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 1221 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: B 70 ASN cc_start: 0.7946 (t0) cc_final: 0.6937 (t0) REVERT: B 72 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6533 (mm) REVERT: B 202 PHE cc_start: 0.6712 (m-80) cc_final: 0.6344 (m-80) outliers start: 31 outliers final: 20 residues processed: 139 average time/residue: 0.0966 time to fit residues: 19.6949 Evaluate side-chains 140 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 540 LEU 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 827 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1019 ARG 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 A residue 1221 GLU 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 212 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: 1.9990 chunk 63 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120444 restraints weight = 15637.871| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.57 r_work: 0.3382 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11844 Z= 0.124 Angle : 0.579 6.907 16290 Z= 0.305 Chirality : 0.043 0.336 1844 Planarity : 0.004 0.081 1936 Dihedral : 17.769 147.002 2015 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 1.55 % Allowed : 16.06 % Favored : 82.39 % 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 (0.24), residues: 1342 helix: 1.08 (0.25), residues: 451 sheet: -0.70 (0.32), residues: 253 loop : -1.54 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.018 0.001 TYR A 399 PHE 0.017 0.001 PHE A 499 TRP 0.013 0.001 TRP A1196 HIS 0.006 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11844) covalent geometry : angle 0.57887 / 0.31 (16290) hydrogen bonds : bond 0.04233 / 2.93 ( 476) hydrogen bonds : angle 4.76361 / 3.31 ( 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 135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8645 (tpt) cc_final: 0.8410 (tpt) REVERT: A 557 TYR cc_start: 0.7329 (p90) cc_final: 0.7109 (p90) REVERT: A 787 GLN cc_start: 0.7511 (tp40) cc_final: 0.7272 (tp40) REVERT: A 827 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7522 (pp) REVERT: A 1007 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 1079 GLN cc_start: 0.7961 (tt0) cc_final: 0.7570 (tp40) REVERT: A 1138 LEU cc_start: 0.7619 (mt) cc_final: 0.7200 (mm) REVERT: A 1166 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7880 (mp) REVERT: B 70 ASN cc_start: 0.7865 (t0) cc_final: 0.6947 (t0) REVERT: B 72 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6500 (mm) REVERT: B 124 GLU cc_start: 0.5907 (tm-30) cc_final: 0.5535 (tm-30) REVERT: B 202 PHE cc_start: 0.6647 (m-80) cc_final: 0.6215 (m-80) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.0971 time to fit residues: 19.1450 Evaluate side-chains 133 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 72 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.167725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118586 restraints weight = 15625.637| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.73 r_work: 0.3357 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11844 Z= 0.183 Angle : 0.611 6.640 16290 Z= 0.322 Chirality : 0.044 0.336 1844 Planarity : 0.005 0.085 1936 Dihedral : 17.803 147.023 2015 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.88 % Rotamer: Outliers : 2.10 % Allowed : 15.78 % 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: -0.85 (0.23), residues: 1342 helix: 1.05 (0.25), residues: 445 sheet: -0.81 (0.32), residues: 257 loop : -1.64 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.019 0.002 TYR A 399 PHE 0.022 0.001 PHE A 499 TRP 0.013 0.001 TRP A1196 HIS 0.008 0.001 HIS A1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (11844) covalent geometry : angle 0.61147 / 0.32 (16290) hydrogen bonds : bond 0.04747 / 3.28 ( 476) hydrogen bonds : angle 4.88481 / 3.40 ( 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 134 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 827 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 1007 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 1079 GLN cc_start: 0.8004 (tt0) cc_final: 0.7602 (tp40) REVERT: A 1138 LEU cc_start: 0.7703 (mt) cc_final: 0.7299 (mm) REVERT: A 1166 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 70 ASN cc_start: 0.7913 (t0) cc_final: 0.7082 (t0) REVERT: B 72 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6599 (mm) REVERT: B 124 GLU cc_start: 0.5920 (tm-30) cc_final: 0.5569 (tm-30) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.0943 time to fit residues: 17.9224 Evaluate side-chains 131 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 72 ILE Chi-restraints excluded: chain B residue 95 THR 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: 8.9990 chunk 112 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.170083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119612 restraints weight = 15674.519| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.63 r_work: 0.3378 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11844 Z= 0.123 Angle : 0.577 6.401 16290 Z= 0.305 Chirality : 0.043 0.339 1844 Planarity : 0.004 0.085 1936 Dihedral : 17.710 145.536 2015 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 1.82 % Allowed : 16.24 % Favored : 81.93 % 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: -0.75 (0.23), residues: 1342 helix: 1.11 (0.25), residues: 450 sheet: -0.74 (0.32), residues: 253 loop : -1.58 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.018 0.001 TYR A 399 PHE 0.020 0.001 PHE A 499 TRP 0.008 0.001 TRP A1196 HIS 0.006 0.001 HIS A1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11844) covalent geometry : angle 0.57708 / 0.30 (16290) hydrogen bonds : bond 0.04118 / 2.86 ( 476) hydrogen bonds : angle 4.72597 / 3.28 ( 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: 20 poor density : 116 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 GLN cc_start: 0.7561 (tp40) cc_final: 0.7341 (tp40) REVERT: A 827 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7562 (pp) REVERT: A 1007 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 1079 GLN cc_start: 0.7982 (tt0) cc_final: 0.7580 (tp40) REVERT: A 1138 LEU cc_start: 0.7639 (mt) cc_final: 0.7235 (mm) REVERT: A 1166 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 70 ASN cc_start: 0.7872 (t0) cc_final: 0.7019 (t0) REVERT: B 72 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6521 (mm) REVERT: B 124 GLU cc_start: 0.5985 (tm-30) cc_final: 0.5557 (tm-30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.0984 time to fit residues: 19.0895 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 935 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1019 ARG 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 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: 3.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.171086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121329 restraints weight = 15706.704| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.74 r_work: 0.3390 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11844 Z= 0.115 Angle : 0.564 7.420 16290 Z= 0.298 Chirality : 0.042 0.342 1844 Planarity : 0.004 0.083 1936 Dihedral : 17.597 144.485 2015 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 1.82 % Allowed : 16.51 % Favored : 81.66 % 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: -0.63 (0.24), residues: 1342 helix: 1.30 (0.26), residues: 444 sheet: -0.70 (0.32), residues: 253 loop : -1.56 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.015 0.001 TYR A 399 PHE 0.019 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 0.00247 / 0.12 (11844) covalent geometry : angle 0.56406 / 0.30 (16290) hydrogen bonds : bond 0.03924 / 2.72 ( 476) hydrogen bonds : angle 4.63630 / 3.22 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.79 seconds wall clock time: 47 minutes 34.33 seconds (2854.33 seconds total)