Starting phenix.real_space_refine on Thu Aug 6 08:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.map" model { file = "/net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klo_62411/08_2026/9klo_62411.cif" } resolution = 2.81 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= 0.028 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 4 9.91 5 P 165 5.49 5 S 36 5.16 5 C 8449 2.51 5 N 2612 2.21 5 O 3106 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: 14372 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10852 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 58, 'TRANS': 1337} Chain breaks: 9 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 16, 'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2201 Inner-chain residues flagged as termini: ['pdbres=" C B 82 "'] Classifications: {'RNA': 103} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 40} Link IDs: {'rna2p': 16, 'rna3p': 86} Chain: "C" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 621 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.46, per 1000 atoms: 0.24 Number of scatterers: 14372 At special positions: 0 Unit cell: (110.285, 120.834, 131.383, 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 4 19.99 S 36 16.00 P 165 15.00 O 3106 8.00 N 2612 7.00 C 8449 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: 1.24 Conformation dependent library (CDL) restraints added in 552.5 milliseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 55.8% alpha, 9.0% beta 49 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 removed outlier: 3.598A pdb=" N ALA A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.514A pdb=" N ALA A 59 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 176 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.534A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.720A pdb=" N MET A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.848A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.903A pdb=" N ASN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Processing helix chain 'A' and resid 337 through 352 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.661A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 418 removed outlier: 3.712A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.559A pdb=" N LEU A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.916A pdb=" N GLU A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.670A pdb=" N PHE A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 6.295A pdb=" N GLU A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.510A pdb=" N GLY A 516 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.972A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.537A pdb=" N ARG A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.732A pdb=" N ALA A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.611A pdb=" N ASP A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.889A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.549A pdb=" N LYS A 745 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 747 " --> pdb=" O ASN A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.642A pdb=" N ALA A 895 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.173A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 958 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.658A pdb=" N SER A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1015 Processing helix chain 'A' and resid 1021 through 1029 Processing helix chain 'A' and resid 1054 through 1073 Proline residue: A1066 - end of helix removed outlier: 3.773A pdb=" N ALA A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 3.768A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1106 " --> pdb=" O TRP A1102 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A1107 " --> pdb=" O MET A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.925A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1120 " --> pdb=" O PRO A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 3.544A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1140 " --> pdb=" O PHE A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 removed outlier: 3.570A pdb=" N LEU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1240 Processing helix chain 'A' and resid 1243 through 1258 Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 3.638A pdb=" N ARG A1272 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A1273 " --> pdb=" O THR A1270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1269 through 1273' Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1325 Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.786A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1375 removed outlier: 3.923A pdb=" N ALA A1375 " --> pdb=" O ILE A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1481 removed outlier: 3.501A pdb=" N TYR A1461 " --> pdb=" O ASP A1457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.687A pdb=" N GLY A 669 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.949A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.238A pdb=" N LEU A 356 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812 removed outlier: 3.626A pdb=" N ARG A 810 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 21.689A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 17.230A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 778 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN A 853 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 776 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 855 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA A 774 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 764 " --> pdb=" O ILE A1218 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A1220 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL A 766 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A1217 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A1265 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A1219 " --> pdb=" O VAL A1265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1391 570 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2688 1.33 - 1.45: 4387 1.45 - 1.57: 7540 1.57 - 1.68: 328 1.68 - 1.80: 56 Bond restraints: 14999 Sorted by residual: bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C4' DT D 27 " pdb=" C3' DT D 27 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.00e-02 1.00e+04 9.26e+00 bond pdb=" C3' DA C 17 " pdb=" C2' DA C 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.06e+00 bond pdb=" C3' DT D 25 " pdb=" C2' DT D 25 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.26e+00 bond pdb=" N TRP A1242 " pdb=" CA TRP A1242 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.20e+00 ... (remaining 14994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 20696 2.60 - 5.19: 340 5.19 - 7.79: 21 7.79 - 10.38: 4 10.38 - 12.98: 2 Bond angle restraints: 21063 Sorted by residual: angle pdb=" O4' G B 92 " pdb=" C1' G B 92 " pdb=" N9 G B 92 " ideal model delta sigma weight residual 108.20 115.77 -7.57 8.00e-01 1.56e+00 8.96e+01 angle pdb=" O3' DG D 11 " pdb=" P DT D 12 " pdb=" O5' DT D 12 " ideal model delta sigma weight residual 104.00 91.02 12.98 1.90e+00 2.77e-01 4.66e+01 angle pdb=" O4' DT C 21 " pdb=" C4' DT C 21 " pdb=" C3' DT C 21 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.56e+01 angle pdb=" C3' DC C 16 " pdb=" O3' DC C 16 " pdb=" P DA C 17 " ideal model delta sigma weight residual 119.70 125.73 -6.03 1.20e+00 6.94e-01 2.52e+01 angle pdb=" O5' C B 60 " pdb=" C5' C B 60 " pdb=" C4' C B 60 " ideal model delta sigma weight residual 109.40 113.24 -3.84 8.00e-01 1.56e+00 2.30e+01 ... (remaining 21058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 8395 35.30 - 70.59: 515 70.59 - 105.89: 42 105.89 - 141.19: 3 141.19 - 176.48: 2 Dihedral angle restraints: 8957 sinusoidal: 4929 harmonic: 4028 Sorted by residual: dihedral pdb=" CA THR A 380 " pdb=" C THR A 380 " pdb=" N ALA A 381 " pdb=" CA ALA A 381 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLN A1362 " pdb=" C GLN A1362 " pdb=" N ALA A1363 " pdb=" CA ALA A1363 " ideal model delta harmonic sigma weight residual 180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" C4' DT D 30 " pdb=" C3' DT D 30 " pdb=" O3' DT D 30 " pdb=" P DT D 31 " ideal model delta sinusoidal sigma weight residual 220.00 43.52 176.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2268 0.119 - 0.239: 116 0.239 - 0.358: 0 0.358 - 0.477: 4 0.477 - 0.596: 3 Chirality restraints: 2391 Sorted by residual: chirality pdb=" P DC C 16 " pdb=" OP1 DC C 16 " pdb=" OP2 DC C 16 " pdb=" O5' DC C 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" P DG D 11 " pdb=" OP1 DG D 11 " pdb=" OP2 DG D 11 " pdb=" O5' DG D 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.26e+00 chirality pdb=" P DT C 15 " pdb=" OP1 DT C 15 " pdb=" OP2 DT C 15 " pdb=" O5' DT C 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 2388 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 92 " -0.049 2.00e-02 2.50e+03 2.25e-02 1.51e+01 pdb=" N9 G B 92 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G B 92 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 92 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 92 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 92 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 92 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 92 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 92 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 92 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 32 " 0.029 2.00e-02 2.50e+03 1.27e-02 4.81e+00 pdb=" N9 G B 32 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G B 32 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 32 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G B 32 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 32 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G B 32 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 32 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 32 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 32 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 32 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 99 " 0.022 2.00e-02 2.50e+03 1.19e-02 3.17e+00 pdb=" N1 U B 99 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U B 99 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U B 99 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 99 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 99 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 99 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U B 99 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U B 99 " -0.003 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 12347 3.23 - 3.79: 22880 3.79 - 4.34: 30775 4.34 - 4.90: 48479 Nonbonded interactions: 114848 Sorted by model distance: nonbonded pdb=" OD1 ASN A 345 " pdb=" NZ LYS A 349 " model vdw 2.122 3.120 nonbonded pdb=" NH1 ARG A 762 " pdb=" OE2 GLU A 780 " model vdw 2.161 3.120 nonbonded pdb=" OG1 THR A 295 " pdb=" OD2 ASP A 323 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A 276 " pdb=" OD1 ASN A 278 " model vdw 2.173 3.040 nonbonded pdb="CA CA A1501 " pdb=" O HOH A1602 " model vdw 2.191 2.510 ... (remaining 114843 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: 2.310 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.780 Find NCS groups from input model: 0.050 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 14999 Z= 0.449 Angle : 0.766 12.977 21063 Z= 0.567 Chirality : 0.057 0.596 2391 Planarity : 0.005 0.041 2112 Dihedral : 19.584 176.484 6347 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.19 % Allowed : 0.65 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.23), residues: 1376 helix: 2.12 (0.20), residues: 687 sheet: -0.18 (0.41), residues: 149 loop : -0.83 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1101 TYR 0.012 0.002 TYR A 978 PHE 0.029 0.002 PHE A1292 TRP 0.014 0.002 TRP A1102 HIS 0.011 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.45 (14999) covalent geometry : angle 0.76583 / 0.57 (21063) hydrogen bonds : bond 0.14039 / 10.01 ( 698) hydrogen bonds : angle 4.86661 / 3.49 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8360 (t0) cc_final: 0.8124 (t0) REVERT: A 301 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7679 (tp30) REVERT: A 521 SER cc_start: 0.9045 (m) cc_final: 0.8752 (t) REVERT: A 750 GLN cc_start: 0.8310 (mp10) cc_final: 0.7850 (mm-40) REVERT: A 975 ASP cc_start: 0.8756 (t0) cc_final: 0.8466 (t0) REVERT: A 1017 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7505 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.6998 (mtt-85) REVERT: A 1039 GLN cc_start: 0.7573 (mt0) cc_final: 0.7231 (mt0) REVERT: A 1159 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8198 (mp0) REVERT: A 1196 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7553 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8157 (tt0) cc_final: 0.7887 (tt0) REVERT: A 1346 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: A 1364 ASP cc_start: 0.8504 (m-30) cc_final: 0.8254 (m-30) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.8370 time to fit residues: 113.2016 Evaluate side-chains 69 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082382 restraints weight = 23717.486| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.25 r_work: 0.2923 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14999 Z= 0.139 Angle : 0.543 10.081 21063 Z= 0.311 Chirality : 0.039 0.306 2391 Planarity : 0.004 0.060 2112 Dihedral : 20.786 178.708 3806 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 7.04 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.23), residues: 1376 helix: 2.49 (0.20), residues: 683 sheet: -0.07 (0.42), residues: 149 loop : -0.67 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1101 TYR 0.016 0.001 TYR A 291 PHE 0.014 0.001 PHE A1292 TRP 0.017 0.001 TRP A 177 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (14999) covalent geometry : angle 0.54287 / 0.31 (21063) hydrogen bonds : bond 0.05857 / 4.08 ( 698) hydrogen bonds : angle 3.85914 / 2.80 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8276 (t0) cc_final: 0.7941 (t0) REVERT: A 301 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7662 (tp30) REVERT: A 521 SER cc_start: 0.9056 (m) cc_final: 0.8762 (t) REVERT: A 719 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6420 (mp10) REVERT: A 750 GLN cc_start: 0.8352 (mp10) cc_final: 0.8000 (mm-40) REVERT: A 975 ASP cc_start: 0.8760 (t0) cc_final: 0.8433 (t0) REVERT: A 1017 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7350 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7232 (mtt-85) REVERT: A 1039 GLN cc_start: 0.7590 (mt0) cc_final: 0.7267 (mt0) REVERT: A 1103 MET cc_start: 0.8752 (tpt) cc_final: 0.8477 (tpp) REVERT: A 1196 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7613 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8273 (tt0) cc_final: 0.7768 (tt0) REVERT: A 1346 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8560 (mm-30) outliers start: 14 outliers final: 3 residues processed: 86 average time/residue: 0.7764 time to fit residues: 71.8317 Evaluate side-chains 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1174 GLU Chi-restraints excluded: chain A residue 1346 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 345 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 = 0.3438 r_free = 0.3438 target = 0.109066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077765 restraints weight = 24010.014| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.24 r_work: 0.2836 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14999 Z= 0.262 Angle : 0.627 10.281 21063 Z= 0.349 Chirality : 0.045 0.347 2391 Planarity : 0.005 0.052 2112 Dihedral : 20.796 179.397 3806 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 10.19 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.23), residues: 1376 helix: 2.26 (0.20), residues: 693 sheet: -0.08 (0.42), residues: 147 loop : -0.80 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1101 TYR 0.032 0.002 TYR A1038 PHE 0.024 0.002 PHE A1292 TRP 0.023 0.002 TRP A 177 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.26 (14999) covalent geometry : angle 0.62655 / 0.35 (21063) hydrogen bonds : bond 0.07070 / 4.93 ( 698) hydrogen bonds : angle 3.90982 / 2.83 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8475 (t0) cc_final: 0.8113 (t0) REVERT: A 254 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: A 301 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7581 (tp30) REVERT: A 521 SER cc_start: 0.9023 (m) cc_final: 0.8680 (t) REVERT: A 719 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6630 (mp10) REVERT: A 750 GLN cc_start: 0.8489 (mp10) cc_final: 0.8081 (mm-40) REVERT: A 975 ASP cc_start: 0.8840 (t0) cc_final: 0.8528 (t0) REVERT: A 1017 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7334 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7447 (mtt-85) REVERT: A 1159 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: A 1196 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7568 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8537 (tt0) cc_final: 0.8051 (tt0) REVERT: A 1346 GLU cc_start: 0.8943 (tp30) cc_final: 0.8675 (mm-30) outliers start: 16 outliers final: 4 residues processed: 83 average time/residue: 0.8373 time to fit residues: 74.8523 Evaluate side-chains 74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 152 optimal weight: 10.9990 chunk 14 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.111999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080704 restraints weight = 23753.808| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.24 r_work: 0.2877 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14999 Z= 0.139 Angle : 0.509 10.147 21063 Z= 0.291 Chirality : 0.038 0.308 2391 Planarity : 0.004 0.039 2112 Dihedral : 20.723 176.858 3803 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.20 % Allowed : 11.58 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.23), residues: 1376 helix: 2.65 (0.20), residues: 685 sheet: -0.05 (0.42), residues: 149 loop : -0.68 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.030 0.001 TYR A1038 PHE 0.012 0.001 PHE A1292 TRP 0.018 0.001 TRP A1102 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (14999) covalent geometry : angle 0.50916 / 0.29 (21063) hydrogen bonds : bond 0.05432 / 3.80 ( 698) hydrogen bonds : angle 3.60910 / 2.61 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8440 (t0) cc_final: 0.8047 (t0) REVERT: A 301 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7525 (tp30) REVERT: A 521 SER cc_start: 0.8975 (m) cc_final: 0.8631 (t) REVERT: A 719 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: A 732 GLN cc_start: 0.8024 (mp10) cc_final: 0.7687 (mm110) REVERT: A 750 GLN cc_start: 0.8482 (mp10) cc_final: 0.8018 (mm-40) REVERT: A 975 ASP cc_start: 0.8796 (t0) cc_final: 0.8496 (t0) REVERT: A 1017 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7339 (mtm-85) REVERT: A 1103 MET cc_start: 0.8614 (tpp) cc_final: 0.8340 (tpp) REVERT: A 1159 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: A 1196 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7563 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8490 (tt0) cc_final: 0.8064 (tt0) REVERT: A 1346 GLU cc_start: 0.8961 (tp30) cc_final: 0.8722 (mm-30) REVERT: A 1362 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7024 (tm-30) outliers start: 13 outliers final: 2 residues processed: 82 average time/residue: 0.8422 time to fit residues: 74.2921 Evaluate side-chains 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1174 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.113790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.082554 restraints weight = 23774.336| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.25 r_work: 0.2900 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14999 Z= 0.123 Angle : 0.482 9.890 21063 Z= 0.275 Chirality : 0.036 0.299 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.621 173.218 3803 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.85 % Allowed : 12.51 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.23), residues: 1376 helix: 2.85 (0.20), residues: 686 sheet: 0.02 (0.44), residues: 139 loop : -0.54 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.020 0.001 TYR A1038 PHE 0.009 0.001 PHE A1292 TRP 0.017 0.001 TRP A1102 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (14999) covalent geometry : angle 0.48182 / 0.27 (21063) hydrogen bonds : bond 0.04802 / 3.38 ( 698) hydrogen bonds : angle 3.39000 / 2.46 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8413 (t0) cc_final: 0.7998 (t0) REVERT: A 172 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7800 (p) REVERT: A 301 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7420 (tp30) REVERT: A 362 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7479 (ttt90) REVERT: A 521 SER cc_start: 0.8979 (m) cc_final: 0.8633 (t) REVERT: A 679 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: A 719 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: A 750 GLN cc_start: 0.8532 (mp10) cc_final: 0.7995 (mm-40) REVERT: A 975 ASP cc_start: 0.8817 (t0) cc_final: 0.8532 (t0) REVERT: A 1017 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7219 (mtm-85) REVERT: A 1103 MET cc_start: 0.8572 (tpp) cc_final: 0.8336 (tpp) REVERT: A 1159 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: A 1196 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7617 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8536 (tt0) cc_final: 0.7973 (tt0) REVERT: A 1362 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.6993 (tm-30) outliers start: 20 outliers final: 2 residues processed: 89 average time/residue: 0.7126 time to fit residues: 68.7327 Evaluate side-chains 79 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.107946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.076593 restraints weight = 23960.029| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.22 r_work: 0.2809 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14999 Z= 0.336 Angle : 0.667 10.215 21063 Z= 0.364 Chirality : 0.048 0.374 2391 Planarity : 0.005 0.043 2112 Dihedral : 20.703 176.473 3803 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.85 % Allowed : 13.25 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.23), residues: 1376 helix: 2.34 (0.20), residues: 693 sheet: -0.15 (0.43), residues: 147 loop : -0.83 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1101 TYR 0.015 0.002 TYR A1387 PHE 0.028 0.002 PHE A1292 TRP 0.018 0.002 TRP A 177 HIS 0.005 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.34 (14999) covalent geometry : angle 0.66724 / 0.36 (21063) hydrogen bonds : bond 0.07333 / 5.11 ( 698) hydrogen bonds : angle 3.82445 / 2.77 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8505 (t0) cc_final: 0.8138 (t0) REVERT: A 254 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: A 301 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7469 (tp30) REVERT: A 362 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (ttt90) REVERT: A 719 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.6761 (mp10) REVERT: A 732 GLN cc_start: 0.8147 (mp10) cc_final: 0.7782 (mm-40) REVERT: A 750 GLN cc_start: 0.8527 (mp10) cc_final: 0.8068 (mm-40) REVERT: A 1017 ARG cc_start: 0.7821 (mtp180) cc_final: 0.7313 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 1196 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7641 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8574 (tt0) cc_final: 0.7952 (tt0) REVERT: A 1362 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 1392 ARG cc_start: 0.8404 (tpp80) cc_final: 0.8192 (tpp80) outliers start: 20 outliers final: 3 residues processed: 83 average time/residue: 0.8103 time to fit residues: 72.4314 Evaluate side-chains 78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 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 = 0.3517 r_free = 0.3517 target = 0.114517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083950 restraints weight = 23616.035| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.22 r_work: 0.2899 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14999 Z= 0.125 Angle : 0.505 10.524 21063 Z= 0.285 Chirality : 0.037 0.303 2391 Planarity : 0.004 0.068 2112 Dihedral : 20.657 174.847 3803 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 13.90 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.23), residues: 1376 helix: 2.80 (0.20), residues: 686 sheet: -0.05 (0.44), residues: 139 loop : -0.67 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 771 TYR 0.017 0.001 TYR A1038 PHE 0.010 0.001 PHE A1292 TRP 0.019 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (14999) covalent geometry : angle 0.50475 / 0.29 (21063) hydrogen bonds : bond 0.05215 / 3.65 ( 698) hydrogen bonds : angle 3.47724 / 2.52 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 172 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8008 (p) REVERT: A 301 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7470 (tp30) REVERT: A 362 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7536 (ttt90) REVERT: A 697 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8122 (ttp-170) REVERT: A 719 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: A 750 GLN cc_start: 0.8521 (mp10) cc_final: 0.8015 (mm-40) REVERT: A 975 ASP cc_start: 0.8808 (t0) cc_final: 0.8502 (t0) REVERT: A 1017 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7432 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: A 1196 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7646 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8639 (tt0) cc_final: 0.8041 (tt0) REVERT: A 1240 MET cc_start: 0.8983 (ptm) cc_final: 0.8746 (ptm) REVERT: A 1362 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: A 1400 GLU cc_start: 0.8881 (tm-30) cc_final: 0.7969 (tm-30) outliers start: 17 outliers final: 2 residues processed: 82 average time/residue: 0.7455 time to fit residues: 66.2230 Evaluate side-chains 74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.111234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079686 restraints weight = 23892.182| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.23 r_work: 0.2867 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14999 Z= 0.210 Angle : 0.550 10.092 21063 Z= 0.308 Chirality : 0.040 0.335 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.627 174.947 3803 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 14.09 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.23), residues: 1376 helix: 2.64 (0.20), residues: 693 sheet: -0.10 (0.44), residues: 139 loop : -0.73 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1101 TYR 0.014 0.002 TYR A1038 PHE 0.017 0.001 PHE A1292 TRP 0.017 0.001 TRP A 177 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (14999) covalent geometry : angle 0.54979 / 0.31 (21063) hydrogen bonds : bond 0.05975 / 4.18 ( 698) hydrogen bonds : angle 3.56931 / 2.58 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8387 (t0) cc_final: 0.8093 (t0) REVERT: A 172 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 301 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7430 (tp30) REVERT: A 362 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7500 (ttt90) REVERT: A 643 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 719 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: A 732 GLN cc_start: 0.8130 (mp10) cc_final: 0.7767 (mm110) REVERT: A 750 GLN cc_start: 0.8534 (mp10) cc_final: 0.8043 (mm-40) REVERT: A 975 ASP cc_start: 0.8812 (t0) cc_final: 0.8516 (t0) REVERT: A 1017 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7408 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 1196 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7666 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8620 (tt0) cc_final: 0.8017 (tt0) REVERT: A 1240 MET cc_start: 0.8957 (ptm) cc_final: 0.8641 (ptm) REVERT: A 1362 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: A 1400 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8017 (tm-30) outliers start: 14 outliers final: 3 residues processed: 79 average time/residue: 0.7718 time to fit residues: 66.1594 Evaluate side-chains 76 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 145 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079570 restraints weight = 23971.077| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.23 r_work: 0.2868 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14999 Z= 0.194 Angle : 0.548 10.128 21063 Z= 0.307 Chirality : 0.040 0.335 2391 Planarity : 0.004 0.045 2112 Dihedral : 20.634 174.908 3803 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.48 % Allowed : 13.99 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.23), residues: 1376 helix: 2.61 (0.20), residues: 694 sheet: -0.13 (0.44), residues: 139 loop : -0.76 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.015 0.002 TYR A1038 PHE 0.018 0.001 PHE A1292 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (14999) covalent geometry : angle 0.54779 / 0.31 (21063) hydrogen bonds : bond 0.05952 / 4.16 ( 698) hydrogen bonds : angle 3.56828 / 2.58 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8056 (tt0) cc_final: 0.7415 (tp30) REVERT: A 150 ASP cc_start: 0.8424 (t0) cc_final: 0.8149 (t0) REVERT: A 172 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8032 (p) REVERT: A 301 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 362 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7495 (ttt90) REVERT: A 643 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 697 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8077 (ttp-170) REVERT: A 719 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: A 732 GLN cc_start: 0.8142 (mp10) cc_final: 0.7768 (mm110) REVERT: A 750 GLN cc_start: 0.8532 (mp10) cc_final: 0.8025 (mm-40) REVERT: A 975 ASP cc_start: 0.8812 (t0) cc_final: 0.8518 (t0) REVERT: A 1017 ARG cc_start: 0.7889 (mtp180) cc_final: 0.7416 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: A 1196 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7625 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8615 (tt0) cc_final: 0.8013 (tt0) REVERT: A 1240 MET cc_start: 0.8922 (ptm) cc_final: 0.8721 (ptm) REVERT: A 1362 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: A 1400 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8026 (tm-30) outliers start: 16 outliers final: 3 residues processed: 81 average time/residue: 0.8005 time to fit residues: 70.0152 Evaluate side-chains 77 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.112238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080708 restraints weight = 23867.148| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.23 r_work: 0.2883 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14999 Z= 0.158 Angle : 0.519 10.122 21063 Z= 0.293 Chirality : 0.038 0.321 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.601 174.132 3803 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.11 % Allowed : 14.46 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.23), residues: 1376 helix: 2.69 (0.20), residues: 694 sheet: -0.09 (0.44), residues: 139 loop : -0.69 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1392 TYR 0.012 0.001 TYR A1038 PHE 0.014 0.001 PHE A1292 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (14999) covalent geometry : angle 0.51864 / 0.29 (21063) hydrogen bonds : bond 0.05505 / 3.86 ( 698) hydrogen bonds : angle 3.49029 / 2.53 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8039 (tt0) cc_final: 0.7393 (tp30) REVERT: A 150 ASP cc_start: 0.8418 (t0) cc_final: 0.8127 (t0) REVERT: A 172 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 301 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7404 (tp30) REVERT: A 362 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7467 (ttt90) REVERT: A 643 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 697 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8094 (ttp-170) REVERT: A 719 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 732 GLN cc_start: 0.8127 (mp10) cc_final: 0.7764 (mm110) REVERT: A 750 GLN cc_start: 0.8529 (mp10) cc_final: 0.8022 (mm-40) REVERT: A 975 ASP cc_start: 0.8808 (t0) cc_final: 0.8526 (t0) REVERT: A 1017 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7412 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 1196 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7621 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8601 (tt0) cc_final: 0.8000 (tt0) REVERT: A 1240 MET cc_start: 0.8900 (ptm) cc_final: 0.8592 (ptm) REVERT: A 1362 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 1400 GLU cc_start: 0.8920 (tm-30) cc_final: 0.7991 (tm-30) outliers start: 12 outliers final: 3 residues processed: 80 average time/residue: 0.7616 time to fit residues: 65.9461 Evaluate side-chains 78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1029 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081594 restraints weight = 23888.944| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.23 r_work: 0.2899 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14999 Z= 0.135 Angle : 0.503 10.077 21063 Z= 0.284 Chirality : 0.037 0.310 2391 Planarity : 0.004 0.041 2112 Dihedral : 20.559 173.032 3803 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.02 % Allowed : 14.64 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.23), residues: 1376 helix: 2.86 (0.20), residues: 687 sheet: -0.05 (0.44), residues: 139 loop : -0.63 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 652 TYR 0.011 0.001 TYR A1038 PHE 0.011 0.001 PHE A1292 TRP 0.018 0.001 TRP A1102 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14999) covalent geometry : angle 0.50314 / 0.28 (21063) hydrogen bonds : bond 0.05107 / 3.59 ( 698) hydrogen bonds : angle 3.40103 / 2.47 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.17 seconds wall clock time: 70 minutes 17.64 seconds (4217.64 seconds total)