Starting phenix.real_space_refine on Fri Jul 3 13:25:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klo_62411/07_2026/9klo_62411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klo_62411/07_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_62411/07_2026/9klo_62411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klo_62411/07_2026/9klo_62411.map" model { file = "/net/cci-nas-00/data/ceres_data/9klo_62411/07_2026/9klo_62411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klo_62411/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 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: 3.41, 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: 1.07 Conformation dependent library (CDL) restraints added in 693.9 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: 2.31 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: 4.58 Time building geometry restraints manager: 1.61 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: 20841 2.60 - 5.19: 195 5.19 - 7.79: 21 7.79 - 10.38: 4 10.38 - 12.98: 2 Bond angle restraints: 21063 Sorted by residual: 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 1.50e+00 4.44e-01 7.48e+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=" 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 1.50e+00 4.44e-01 2.55e+01 angle pdb=" O4' DT D 27 " pdb=" C4' DT D 27 " pdb=" C3' DT D 27 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+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: 2348 0.119 - 0.239: 36 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 3.250 ... (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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- 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= 0.440 Angle : 0.706 12.977 21063 Z= 0.513 Chirality : 0.051 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 0.00660 / 0.44 (14999) covalent geometry : angle 0.70584 / 0.51 (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 : 0.454 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: 0.8358 time to fit residues: 113.0399 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 : 0.465 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.113337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082199 restraints weight = 23748.085| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.24 r_work: 0.2931 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14999 Z= 0.141 Angle : 0.539 10.140 21063 Z= 0.310 Chirality : 0.038 0.377 2391 Planarity : 0.004 0.054 2112 Dihedral : 20.799 178.735 3806 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.48 % Allowed : 6.95 % Favored : 91.57 % 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: 1.48 (0.23), residues: 1376 helix: 2.48 (0.20), residues: 683 sheet: -0.11 (0.42), residues: 149 loop : -0.67 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.016 0.001 TYR A 291 PHE 0.014 0.001 PHE A1292 TRP 0.016 0.001 TRP A1102 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (14999) covalent geometry : angle 0.53882 / 0.31 (21063) hydrogen bonds : bond 0.05927 / 4.14 ( 698) hydrogen bonds : angle 3.87453 / 2.81 ( 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 93 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.467 Fit side-chains REVERT: A 150 ASP cc_start: 0.8409 (t0) cc_final: 0.8091 (t0) REVERT: A 301 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7650 (tp30) REVERT: A 521 SER cc_start: 0.9055 (m) cc_final: 0.8755 (t) REVERT: A 697 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8180 (ttp-170) REVERT: A 719 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: A 750 GLN cc_start: 0.8470 (mp10) cc_final: 0.8090 (mm-40) REVERT: A 975 ASP cc_start: 0.8823 (t0) cc_final: 0.8507 (t0) REVERT: A 1017 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7379 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7422 (mtt-85) REVERT: A 1039 GLN cc_start: 0.7586 (mt0) cc_final: 0.7258 (mt0) REVERT: A 1103 MET cc_start: 0.8837 (tpt) cc_final: 0.8569 (tpp) REVERT: A 1159 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8089 (mp0) REVERT: A 1196 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7578 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8430 (tt0) cc_final: 0.8029 (tt0) REVERT: A 1346 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8706 (mm-30) outliers start: 16 outliers final: 3 residues processed: 86 average time/residue: 0.8416 time to fit residues: 77.9988 Evaluate side-chains 74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.079113 restraints weight = 23970.704| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.25 r_work: 0.2874 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14999 Z= 0.209 Angle : 0.559 9.930 21063 Z= 0.319 Chirality : 0.041 0.371 2391 Planarity : 0.004 0.049 2112 Dihedral : 20.794 178.385 3806 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 9.55 % Favored : 88.97 % 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: 1.44 (0.23), residues: 1376 helix: 2.41 (0.20), residues: 692 sheet: -0.09 (0.42), residues: 147 loop : -0.70 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1101 TYR 0.027 0.002 TYR A1038 PHE 0.020 0.002 PHE A1292 TRP 0.021 0.002 TRP A 177 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (14999) covalent geometry : angle 0.55858 / 0.32 (21063) hydrogen bonds : bond 0.06299 / 4.40 ( 698) hydrogen bonds : angle 3.78533 / 2.74 ( 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 88 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8424 (t0) cc_final: 0.8060 (t0) REVERT: A 254 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: A 301 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7584 (tp30) REVERT: A 453 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8081 (mtt-85) REVERT: A 521 SER cc_start: 0.9031 (m) cc_final: 0.8695 (t) REVERT: A 719 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: A 732 GLN cc_start: 0.8166 (mp10) cc_final: 0.7795 (mm110) REVERT: A 750 GLN cc_start: 0.8502 (mp10) cc_final: 0.8076 (mm-40) REVERT: A 975 ASP cc_start: 0.8803 (t0) cc_final: 0.8471 (t0) REVERT: A 1017 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7348 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7461 (mtt-85) REVERT: A 1159 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8131 (mp0) REVERT: A 1196 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7639 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8541 (tt0) cc_final: 0.8072 (tt0) REVERT: A 1346 GLU cc_start: 0.8958 (tp30) cc_final: 0.8755 (mm-30) outliers start: 16 outliers final: 2 residues processed: 83 average time/residue: 0.7821 time to fit residues: 69.8249 Evaluate side-chains 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 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: 4.9990 chunk 87 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.111841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080571 restraints weight = 23811.770| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.24 r_work: 0.2887 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1535 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= 0.150 Angle : 0.506 10.033 21063 Z= 0.291 Chirality : 0.038 0.356 2391 Planarity : 0.004 0.043 2112 Dihedral : 20.734 176.503 3803 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 11.58 % Favored : 87.12 % 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: 2.68 (0.20), residues: 685 sheet: -0.08 (0.42), residues: 149 loop : -0.62 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.026 0.001 TYR A1038 PHE 0.013 0.001 PHE A1292 TRP 0.017 0.001 TRP A1102 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (14999) covalent geometry : angle 0.50627 / 0.29 (21063) hydrogen bonds : bond 0.05443 / 3.81 ( 698) hydrogen bonds : angle 3.61462 / 2.63 ( 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 87 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8423 (t0) cc_final: 0.7999 (t0) REVERT: A 172 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 301 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7503 (tp30) REVERT: A 453 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7826 (mtt-85) REVERT: A 521 SER cc_start: 0.8977 (m) cc_final: 0.8633 (t) REVERT: A 719 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: A 750 GLN cc_start: 0.8478 (mp10) cc_final: 0.8014 (mm-40) REVERT: A 975 ASP cc_start: 0.8794 (t0) cc_final: 0.8477 (t0) REVERT: A 1017 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7216 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8089 (mp0) REVERT: A 1196 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7546 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8477 (tt0) cc_final: 0.7998 (tt0) REVERT: A 1346 GLU cc_start: 0.8985 (tp30) cc_final: 0.8748 (mm-30) REVERT: A 1362 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7021 (tm-30) outliers start: 14 outliers final: 2 residues processed: 83 average time/residue: 0.8213 time to fit residues: 73.3376 Evaluate side-chains 74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 719 GLN 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: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081232 restraints weight = 23797.567| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.25 r_work: 0.2895 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1725 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= 0.138 Angle : 0.487 10.019 21063 Z= 0.281 Chirality : 0.037 0.349 2391 Planarity : 0.004 0.040 2112 Dihedral : 20.658 174.437 3803 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.67 % Allowed : 12.14 % Favored : 86.19 % 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: 1.74 (0.23), residues: 1376 helix: 2.71 (0.20), residues: 694 sheet: -0.03 (0.42), residues: 149 loop : -0.63 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.019 0.001 TYR A1038 PHE 0.012 0.001 PHE A1292 TRP 0.016 0.001 TRP A1102 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (14999) covalent geometry : angle 0.48696 / 0.28 (21063) hydrogen bonds : bond 0.05087 / 3.57 ( 698) hydrogen bonds : angle 3.49292 / 2.54 ( 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 91 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8418 (t0) cc_final: 0.7993 (t0) REVERT: A 301 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7433 (tp30) REVERT: A 362 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7442 (ttt90) REVERT: A 453 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7811 (mtt-85) REVERT: A 521 SER cc_start: 0.8974 (m) cc_final: 0.8626 (t) REVERT: A 679 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 719 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: A 750 GLN cc_start: 0.8500 (mp10) cc_final: 0.8004 (mm-40) REVERT: A 975 ASP cc_start: 0.8781 (t0) cc_final: 0.8467 (t0) REVERT: A 1017 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7183 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8082 (mp0) REVERT: A 1196 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7562 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8484 (tt0) cc_final: 0.7867 (tt0) REVERT: A 1346 GLU cc_start: 0.8985 (tp30) cc_final: 0.8765 (mm-30) REVERT: A 1362 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.6927 (tm-30) outliers start: 18 outliers final: 6 residues processed: 86 average time/residue: 0.6984 time to fit residues: 65.0166 Evaluate side-chains 81 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 679 GLU 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 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1335 MET 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: 0.9980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.110369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.079066 restraints weight = 23840.852| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.24 r_work: 0.2832 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14999 Z= 0.213 Angle : 0.547 10.058 21063 Z= 0.309 Chirality : 0.040 0.359 2391 Planarity : 0.004 0.040 2112 Dihedral : 20.665 175.252 3803 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.67 % Allowed : 12.70 % 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: 1.63 (0.23), residues: 1376 helix: 2.61 (0.20), residues: 693 sheet: -0.11 (0.42), residues: 147 loop : -0.66 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1101 TYR 0.016 0.002 TYR A1038 PHE 0.019 0.001 PHE A1292 TRP 0.017 0.002 TRP A 177 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (14999) covalent geometry : angle 0.54735 / 0.31 (21063) hydrogen bonds : bond 0.05997 / 4.18 ( 698) hydrogen bonds : angle 3.62099 / 2.63 ( 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 89 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8461 (t0) cc_final: 0.8033 (t0) REVERT: A 172 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7796 (p) REVERT: A 254 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: A 301 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7453 (tp30) REVERT: A 362 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7428 (ttt90) REVERT: A 453 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7870 (mtt-85) REVERT: A 521 SER cc_start: 0.8954 (m) cc_final: 0.8596 (t) REVERT: A 719 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: A 750 GLN cc_start: 0.8544 (mp10) cc_final: 0.8049 (mm-40) REVERT: A 975 ASP cc_start: 0.8806 (t0) cc_final: 0.8508 (t0) REVERT: A 1017 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7294 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8112 (mp0) REVERT: A 1196 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7591 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8526 (tt0) cc_final: 0.8094 (tt0) REVERT: A 1346 GLU cc_start: 0.8977 (tp30) cc_final: 0.8694 (mm-30) REVERT: A 1362 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7159 (tm-30) outliers start: 18 outliers final: 3 residues processed: 84 average time/residue: 0.7341 time to fit residues: 66.5330 Evaluate side-chains 80 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR 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 1174 GLU Chi-restraints excluded: chain A residue 1260 LEU 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: 3.9990 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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 = 0.113634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082139 restraints weight = 23897.973| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.24 r_work: 0.2918 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1913 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= 0.124 Angle : 0.479 10.069 21063 Z= 0.276 Chirality : 0.036 0.344 2391 Planarity : 0.003 0.040 2112 Dihedral : 20.617 173.507 3803 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 13.16 % Favored : 85.54 % 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: 1.86 (0.23), residues: 1376 helix: 2.87 (0.20), residues: 688 sheet: -0.06 (0.43), residues: 139 loop : -0.59 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.016 0.001 TYR A1038 PHE 0.009 0.001 PHE A1292 TRP 0.017 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 0.47922 / 0.28 (21063) hydrogen bonds : bond 0.04859 / 3.41 ( 698) hydrogen bonds : angle 3.41666 / 2.48 ( 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: 14 poor density : 75 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8016 (tt0) cc_final: 0.7627 (tm-30) REVERT: A 172 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7907 (p) REVERT: A 301 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7432 (tp30) REVERT: A 362 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7478 (ttt90) REVERT: A 453 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: A 697 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8135 (ttp-170) REVERT: A 719 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6738 (mp10) REVERT: A 750 GLN cc_start: 0.8554 (mp10) cc_final: 0.8011 (mm-40) REVERT: A 975 ASP cc_start: 0.8803 (t0) cc_final: 0.8501 (t0) REVERT: A 1017 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7369 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8133 (mp0) REVERT: A 1196 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7609 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8570 (tt0) cc_final: 0.7977 (tt0) REVERT: A 1362 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7025 (tm-30) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 0.7504 time to fit residues: 68.8995 Evaluate side-chains 79 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG 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 1174 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.112303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081411 restraints weight = 23621.669| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.17 r_work: 0.2902 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1920 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 : 0.500 10.057 21063 Z= 0.286 Chirality : 0.037 0.350 2391 Planarity : 0.004 0.042 2112 Dihedral : 20.588 173.278 3803 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.85 % Allowed : 12.79 % Favored : 85.36 % 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: 1.77 (0.23), residues: 1376 helix: 2.77 (0.20), residues: 694 sheet: -0.08 (0.43), residues: 139 loop : -0.64 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.014 0.001 TYR A1038 PHE 0.013 0.001 PHE A1292 TRP 0.016 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (14999) covalent geometry : angle 0.50017 / 0.29 (21063) hydrogen bonds : bond 0.05235 / 3.67 ( 698) hydrogen bonds : angle 3.43670 / 2.49 ( 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 90 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8341 (t0) cc_final: 0.8063 (t0) REVERT: A 172 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 254 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 301 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 362 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7478 (ttt90) REVERT: A 453 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7935 (mtt-85) REVERT: A 719 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: A 750 GLN cc_start: 0.8541 (mp10) cc_final: 0.8038 (mm-40) REVERT: A 975 ASP cc_start: 0.8807 (t0) cc_final: 0.8513 (t0) REVERT: A 1017 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7382 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8157 (mp0) REVERT: A 1196 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7602 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8590 (tt0) cc_final: 0.7999 (tt0) REVERT: A 1362 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7121 (tm-30) outliers start: 20 outliers final: 6 residues processed: 85 average time/residue: 0.7622 time to fit residues: 70.0873 Evaluate side-chains 78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 172 THR 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 1006 MET Chi-restraints excluded: chain A residue 1174 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: 0.2980 chunk 31 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.114313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082855 restraints weight = 23913.689| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.24 r_work: 0.2930 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.002 0.027 14999 Z= 0.113 Angle : 0.477 10.139 21063 Z= 0.273 Chirality : 0.036 0.339 2391 Planarity : 0.004 0.095 2112 Dihedral : 20.582 172.579 3803 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.39 % Allowed : 13.35 % Favored : 85.26 % 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: 1.98 (0.23), residues: 1376 helix: 2.98 (0.20), residues: 687 sheet: -0.04 (0.43), residues: 139 loop : -0.52 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 771 TYR 0.014 0.001 TYR A1038 PHE 0.009 0.001 PHE A1292 TRP 0.017 0.001 TRP A1102 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.11 (14999) covalent geometry : angle 0.47686 / 0.27 (21063) hydrogen bonds : bond 0.04682 / 3.28 ( 698) hydrogen bonds : angle 3.34095 / 2.43 ( 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 89 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8017 (tt0) cc_final: 0.7627 (tm-30) REVERT: A 136 MET cc_start: 0.9052 (tpp) cc_final: 0.8849 (mmm) REVERT: A 150 ASP cc_start: 0.8356 (t0) cc_final: 0.8049 (t0) REVERT: A 172 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7984 (p) REVERT: A 301 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7420 (tp30) REVERT: A 362 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7465 (ttt90) REVERT: A 453 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7912 (mtt-85) REVERT: A 697 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8130 (ttp-170) REVERT: A 719 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: A 750 GLN cc_start: 0.8554 (mp10) cc_final: 0.8004 (mm-40) REVERT: A 975 ASP cc_start: 0.8799 (t0) cc_final: 0.8504 (t0) REVERT: A 1017 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7274 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8126 (mp0) REVERT: A 1196 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7601 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8553 (tt0) cc_final: 0.8001 (tt0) REVERT: A 1286 ASP cc_start: 0.8544 (m-30) cc_final: 0.8333 (m-30) REVERT: A 1362 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7022 (tm-30) outliers start: 15 outliers final: 5 residues processed: 85 average time/residue: 0.7411 time to fit residues: 68.0383 Evaluate side-chains 79 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG 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 1174 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=1.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.109456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.078098 restraints weight = 23697.779| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.24 r_work: 0.2847 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14999 Z= 0.255 Angle : 0.571 10.232 21063 Z= 0.321 Chirality : 0.042 0.359 2391 Planarity : 0.005 0.041 2112 Dihedral : 20.602 174.478 3803 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.39 % Allowed : 13.35 % Favored : 85.26 % 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: 1.64 (0.23), residues: 1376 helix: 2.62 (0.20), residues: 694 sheet: -0.11 (0.44), residues: 137 loop : -0.65 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1101 TYR 0.014 0.002 TYR A1038 PHE 0.021 0.002 PHE A1292 TRP 0.015 0.002 TRP A 177 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (14999) covalent geometry : angle 0.57146 / 0.32 (21063) hydrogen bonds : bond 0.06269 / 4.37 ( 698) hydrogen bonds : angle 3.60607 / 2.61 ( 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: 15 poor density : 68 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8395 (t0) cc_final: 0.8078 (t0) REVERT: A 172 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 254 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: A 301 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 362 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7377 (ttt90) REVERT: A 453 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7981 (mtt-85) REVERT: A 719 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: A 750 GLN cc_start: 0.8507 (mp10) cc_final: 0.8008 (mm-40) REVERT: A 975 ASP cc_start: 0.8815 (t0) cc_final: 0.8536 (t0) REVERT: A 1017 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7306 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8100 (mp0) REVERT: A 1196 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7587 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8530 (tt0) cc_final: 0.7907 (tt0) REVERT: A 1362 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7193 (tm-30) outliers start: 15 outliers final: 4 residues processed: 79 average time/residue: 0.8275 time to fit residues: 70.4544 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 172 THR 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 1174 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: 0.0970 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.114481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083712 restraints weight = 23606.371| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.20 r_work: 0.2933 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14999 Z= 0.111 Angle : 0.479 10.118 21063 Z= 0.274 Chirality : 0.035 0.335 2391 Planarity : 0.004 0.054 2112 Dihedral : 20.564 172.384 3803 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.93 % Allowed : 13.81 % Favored : 85.26 % 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: 1.96 (0.23), residues: 1376 helix: 2.95 (0.20), residues: 687 sheet: -0.03 (0.43), residues: 139 loop : -0.54 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.009 0.001 TYR A1038 PHE 0.007 0.001 PHE A1292 TRP 0.018 0.001 TRP A 177 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.11 (14999) covalent geometry : angle 0.47862 / 0.27 (21063) hydrogen bonds : bond 0.04587 / 3.22 ( 698) hydrogen bonds : angle 3.33495 / 2.43 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.58 seconds wall clock time: 74 minutes 5.76 seconds (4445.76 seconds total)