Starting phenix.real_space_refine on Fri Sep 11 16:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iv6_9742/09_2026/6iv6_9742.map" } resolution = 3.6 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 21 5.16 5 C 6406 2.51 5 N 1722 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10158 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 9611 Classifications: {'peptide': 1209} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 4, 'PTRANS': 35, 'TRANS': 1169} Chain breaks: 4 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ALY:plan-2': 4, 'ASP:plan': 5, 'GLU:plan': 9, 'GLN:plan1': 7, 'ASN:plan1': 4, 'TYR:plan': 5, 'PHE:plan': 2, 'HIS:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 178 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 547 Classifications: {'RNAv2': 26} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 8, 'rna3p': 17} Time building chain proxies: 2.06, per 1000 atoms: 0.20 Number of scatterers: 10158 At special positions: 0 Unit cell: (110.39, 101.26, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 26 15.00 O 1983 8.00 N 1722 7.00 C 6406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 207.3 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 42.0% alpha, 7.9% beta 6 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 34 through 65 removed outlier: 4.460A pdb=" N GLN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.616A pdb=" N LEU A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 removed outlier: 4.212A pdb=" N GLU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.864A pdb=" N TYR A 166 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 168 " --> pdb=" O THR A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 168' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.949A pdb=" N ASN A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.794A pdb=" N ARG A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.676A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.838A pdb=" N ILE A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.699A pdb=" N LEU A 233 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.891A pdb=" N LEU A 244 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.654A pdb=" N ALA A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.503A pdb=" N ASN A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.934A pdb=" N VAL A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 3.664A pdb=" N GLY A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.850A pdb=" N VAL A 384 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 385 " --> pdb=" O VAL A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 385' Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.667A pdb=" N TYR A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 432' Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.656A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 removed outlier: 4.002A pdb=" N GLU A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.689A pdb=" N LEU A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.981A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.645A pdb=" N LEU A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 657 Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.603A pdb=" N LYS A 662 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 663 " --> pdb=" O THR A 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 659 through 663' Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.848A pdb=" N ILE A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.554A pdb=" N VAL A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Proline residue: A 714 - end of helix Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.534A pdb=" N ILE A 729 " --> pdb=" O ASN A 725 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 749 removed outlier: 3.731A pdb=" N SER A 749 " --> pdb=" O LYS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 764 removed outlier: 3.519A pdb=" N TYR A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 772 removed outlier: 3.514A pdb=" N LEU A 772 " --> pdb=" O GLU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 4.124A pdb=" N GLN A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.538A pdb=" N ILE A 924 " --> pdb=" O ASP A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 962 removed outlier: 3.855A pdb=" N THR A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 939 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 4.006A pdb=" N ASN A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1072 removed outlier: 3.778A pdb=" N GLN A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.602A pdb=" N ILE A1158 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1154 through 1159' Processing helix chain 'A' and resid 1165 through 1179 removed outlier: 3.667A pdb=" N LEU A1177 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1238 removed outlier: 3.579A pdb=" N GLY A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A1225 " --> pdb=" O GLY A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1260 removed outlier: 3.552A pdb=" N LEU A1255 " --> pdb=" O ASN A1251 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 721 through 724 removed outlier: 3.527A pdb=" N MET A 621 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 587 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR A 594 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564 removed outlier: 4.624A pdb=" N ILE A 785 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 625 Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 897 removed outlier: 6.879A pdb=" N VAL A 885 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN A 895 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A 883 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER A 897 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 881 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 968 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ARG A 875 " --> pdb=" O GLU A 968 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 900 through 905 removed outlier: 3.755A pdb=" N ILE A 901 " --> pdb=" O THR A 913 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 913 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR A 903 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET A 911 " --> pdb=" O THR A 903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1077 through 1079 removed outlier: 3.818A pdb=" N ILE A1090 " --> pdb=" O TRP A1106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A1106 " --> pdb=" O ILE A1090 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1181 through 1183 294 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.94 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: 2749 1.33 - 1.45: 2062 1.45 - 1.57: 5529 1.57 - 1.69: 52 1.69 - 1.81: 35 Bond restraints: 10427 Sorted by residual: bond pdb=" C ALY A 153 " pdb=" O ALY A 153 " ideal model delta sigma weight residual 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C ALY A 635 " pdb=" O ALY A 635 " ideal model delta sigma weight residual 1.231 1.360 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C ALY A 816 " pdb=" O ALY A 816 " ideal model delta sigma weight residual 1.231 1.359 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" N GLN A 281 " pdb=" CA GLN A 281 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" N ASN A 280 " pdb=" CA ASN A 280 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.44e+00 ... (remaining 10422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13876 3.08 - 6.17: 284 6.17 - 9.25: 32 9.25 - 12.33: 9 12.33 - 15.41: 3 Bond angle restraints: 14204 Sorted by residual: angle pdb=" C THR A 518 " pdb=" N THR A 519 " pdb=" CA THR A 519 " ideal model delta sigma weight residual 121.70 136.98 -15.28 1.80e+00 3.09e-01 7.21e+01 angle pdb=" O ALY A 635 " pdb=" C ALY A 635 " pdb=" N VAL A 636 " ideal model delta sigma weight residual 123.00 111.47 11.53 1.60e+00 3.91e-01 5.19e+01 angle pdb=" CA ALY A 153 " pdb=" C ALY A 153 " pdb=" O ALY A 153 " ideal model delta sigma weight residual 120.80 109.97 10.83 1.70e+00 3.46e-01 4.06e+01 angle pdb=" C GLY A 120 " pdb=" N TYR A 121 " pdb=" CA TYR A 121 " ideal model delta sigma weight residual 121.54 132.60 -11.06 1.91e+00 2.74e-01 3.35e+01 angle pdb=" C GLN A 281 " pdb=" N HIS A 282 " pdb=" CA HIS A 282 " ideal model delta sigma weight residual 121.70 131.91 -10.21 1.80e+00 3.09e-01 3.22e+01 ... (remaining 14199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5308 17.21 - 34.42: 632 34.42 - 51.63: 151 51.63 - 68.84: 61 68.84 - 86.05: 23 Dihedral angle restraints: 6175 sinusoidal: 2635 harmonic: 3540 Sorted by residual: dihedral pdb=" C4' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " pdb=" C1' U G 15 " ideal model delta sinusoidal sigma weight residual 36.34 -36.72 73.06 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G G 13 " pdb=" C3' G G 13 " pdb=" C2' G G 13 " pdb=" C1' G G 13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.46 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' U G 12 " pdb=" C3' U G 12 " pdb=" C2' U G 12 " pdb=" C1' U G 12 " ideal model delta sinusoidal sigma weight residual 36.35 -36.09 72.43 1 3.10e+00 1.04e-01 6.97e+02 ... (remaining 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1297 0.074 - 0.148: 198 0.148 - 0.223: 36 0.223 - 0.297: 32 0.297 - 0.371: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A1029 " pdb=" CA ILE A1029 " pdb=" CG1 ILE A1029 " pdb=" CG2 ILE A1029 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C2' U G 5 " pdb=" C3' U G 5 " pdb=" O2' U G 5 " pdb=" C1' U G 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' A G 3 " pdb=" C3' A G 3 " pdb=" O2' A G 3 " pdb=" C1' A G 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 1561 not shown) Planarity restraints: 1754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALY A 153 " 0.080 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C ALY A 153 " -0.269 2.00e-02 2.50e+03 pdb=" O ALY A 153 " 0.090 2.00e-02 2.50e+03 pdb=" N LEU A 154 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALY A 635 " 0.083 2.00e-02 2.50e+03 1.53e-01 2.35e+02 pdb=" C ALY A 635 " -0.265 2.00e-02 2.50e+03 pdb=" O ALY A 635 " 0.089 2.00e-02 2.50e+03 pdb=" N VAL A 636 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 112 " -0.023 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C GLY A 112 " 0.082 2.00e-02 2.50e+03 pdb=" O GLY A 112 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN A 113 " -0.028 2.00e-02 2.50e+03 ... (remaining 1751 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2513 2.79 - 3.32: 8624 3.32 - 3.84: 15950 3.84 - 4.37: 18856 4.37 - 4.90: 31975 Nonbonded interactions: 77918 Sorted by model distance: nonbonded pdb=" OH TYR A 623 " pdb=" O LEU A 779 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 10 " pdb=" OD1 ASN A 998 " model vdw 2.318 3.040 nonbonded pdb=" O THR A 208 " pdb=" OG SER A 214 " model vdw 2.321 3.040 nonbonded pdb=" O LYS A 512 " pdb=" OG1 THR A 515 " model vdw 2.338 3.040 nonbonded pdb=" OH TYR A 353 " pdb=" OD1 ASN A 522 " model vdw 2.342 3.040 ... (remaining 77913 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 group one per residue 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: 1.230 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.800 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.005 0.132 10427 Z= 0.281 Angle : 1.075 15.413 14204 Z= 0.584 Chirality : 0.066 0.371 1564 Planarity : 0.008 0.155 1754 Dihedral : 17.177 86.052 3897 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 0.61 % Allowed : 8.38 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.17 (0.17), residues: 1187 helix: -4.23 (0.11), residues: 426 sheet: -2.75 (0.43), residues: 124 loop : -3.01 (0.19), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.034 0.002 TYR A 327 PHE 0.020 0.002 PHE A 18 TRP 0.015 0.002 TRP A1042 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.28 (10427) covalent geometry : angle 1.07497 / 0.58 (14204) hydrogen bonds : bond 0.27162 / 18.24 ( 308) hydrogen bonds : angle 10.00735 / 6.82 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7129 (t0) cc_final: 0.6854 (t0) REVERT: A 162 LYS cc_start: 0.6627 (mttt) cc_final: 0.5393 (mmtt) REVERT: A 293 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6771 (mtm180) REVERT: A 380 TYR cc_start: 0.4658 (m-80) cc_final: 0.2956 (t80) REVERT: A 498 LYS cc_start: 0.7230 (pptt) cc_final: 0.5648 (mmmm) REVERT: A 560 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6464 (mt-10) REVERT: A 894 GLU cc_start: 0.8383 (pt0) cc_final: 0.8165 (tt0) REVERT: A 921 LYS cc_start: 0.5492 (ttpt) cc_final: 0.5243 (mtmt) REVERT: A 1061 TYR cc_start: 0.7244 (t80) cc_final: 0.6788 (t80) REVERT: A 1104 GLN cc_start: 0.7497 (mt0) cc_final: 0.7268 (mt0) REVERT: A 1113 ASP cc_start: 0.7285 (t70) cc_final: 0.6657 (t70) REVERT: A 1115 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7241 (mmt90) REVERT: A 1243 ASN cc_start: 0.5276 (t0) cc_final: 0.5013 (t0) outliers start: 6 outliers final: 2 residues processed: 171 average time/residue: 0.1006 time to fit residues: 23.9324 Evaluate side-chains 117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 1216 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 204 GLN A 219 GLN A 236 HIS ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 279 HIS A 296 HIS A 324 ASN A 506 ASN A 526 ASN A 612 ASN A 642 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 742 GLN A 843 ASN A 859 ASN A 869 ASN A 910 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.189077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.184473 restraints weight = 12471.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.183656 restraints weight = 19543.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.172157 restraints weight = 22929.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.171496 restraints weight = 25968.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.171391 restraints weight = 21042.582| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10427 Z= 0.203 Angle : 0.827 11.638 14204 Z= 0.389 Chirality : 0.061 0.919 1564 Planarity : 0.005 0.048 1754 Dihedral : 11.901 137.103 1624 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.83 % Allowed : 14.53 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -3.89 (0.19), residues: 1187 helix: -2.42 (0.19), residues: 425 sheet: -2.69 (0.45), residues: 121 loop : -2.71 (0.20), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 104 TYR 0.023 0.002 TYR A 121 PHE 0.018 0.002 PHE A 18 TRP 0.009 0.002 TRP A 575 HIS 0.011 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (10427) covalent geometry : angle 0.82736 / 0.39 (14204) hydrogen bonds : bond 0.05107 / 3.36 ( 308) hydrogen bonds : angle 5.89793 / 3.91 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.7930 (ttm) cc_final: 0.7672 (ttt) REVERT: A 162 LYS cc_start: 0.6989 (mttt) cc_final: 0.5935 (mmtt) REVERT: A 293 ARG cc_start: 0.7332 (mtp180) cc_final: 0.7092 (mtt180) REVERT: A 328 ARG cc_start: 0.5154 (mmm160) cc_final: 0.4807 (mtp-110) REVERT: A 380 TYR cc_start: 0.4880 (m-80) cc_final: 0.3333 (t80) REVERT: A 460 LYS cc_start: 0.4960 (mmtp) cc_final: 0.4715 (mmtt) REVERT: A 498 LYS cc_start: 0.7906 (pptt) cc_final: 0.6823 (tptm) REVERT: A 560 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 921 LYS cc_start: 0.6415 (ttpt) cc_final: 0.5971 (mttt) REVERT: A 1115 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7709 (mmt90) REVERT: A 1208 LEU cc_start: 0.7037 (tt) cc_final: 0.6716 (tp) outliers start: 28 outliers final: 16 residues processed: 141 average time/residue: 0.0837 time to fit residues: 17.1266 Evaluate side-chains 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 104 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 324 ASN A 459 GLN A 526 ASN A 686 HIS ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN A1089 HIS A1198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.191242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.187274 restraints weight = 12576.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.186698 restraints weight = 17549.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.186170 restraints weight = 20679.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.185822 restraints weight = 21354.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.178348 restraints weight = 18967.937| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10427 Z= 0.119 Angle : 0.672 10.313 14204 Z= 0.319 Chirality : 0.052 0.529 1564 Planarity : 0.003 0.036 1754 Dihedral : 11.606 147.703 1622 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.72 % Allowed : 18.16 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.99 (0.22), residues: 1187 helix: -1.21 (0.23), residues: 429 sheet: -2.48 (0.46), residues: 123 loop : -2.48 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.024 0.001 TYR A 121 PHE 0.016 0.001 PHE A 510 TRP 0.011 0.002 TRP A 575 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10427) covalent geometry : angle 0.67183 / 0.32 (14204) hydrogen bonds : bond 0.03743 / 2.43 ( 308) hydrogen bonds : angle 5.13018 / 3.39 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6063 (tmm) REVERT: A 42 MET cc_start: 0.7826 (ttm) cc_final: 0.7572 (ttt) REVERT: A 65 MET cc_start: 0.7488 (mmt) cc_final: 0.7064 (mmp) REVERT: A 162 LYS cc_start: 0.6854 (mttt) cc_final: 0.6006 (mmtt) REVERT: A 328 ARG cc_start: 0.4724 (mmm160) cc_final: 0.4230 (mtp-110) REVERT: A 380 TYR cc_start: 0.4749 (m-80) cc_final: 0.3742 (t80) REVERT: A 460 LYS cc_start: 0.5255 (mmtp) cc_final: 0.4741 (mmtp) REVERT: A 498 LYS cc_start: 0.7763 (pptt) cc_final: 0.6786 (tptm) REVERT: A 921 LYS cc_start: 0.6219 (ttpt) cc_final: 0.5963 (mttt) REVERT: A 1115 ARG cc_start: 0.7932 (mmt-90) cc_final: 0.7639 (mmt90) REVERT: A 1208 LEU cc_start: 0.6882 (tt) cc_final: 0.6589 (tp) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.0946 time to fit residues: 17.8689 Evaluate side-chains 111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 957 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 61 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 526 ASN A 759 HIS A 869 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.191244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.187377 restraints weight = 12579.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.176911 restraints weight = 21396.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.174786 restraints weight = 22470.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.174471 restraints weight = 23323.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.174569 restraints weight = 20204.828| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10427 Z= 0.120 Angle : 0.649 10.947 14204 Z= 0.307 Chirality : 0.050 0.390 1564 Planarity : 0.003 0.033 1754 Dihedral : 11.523 143.609 1622 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.04 % Allowed : 18.77 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.54 (0.23), residues: 1187 helix: -0.68 (0.24), residues: 445 sheet: -2.25 (0.47), residues: 125 loop : -2.36 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.030 0.001 TYR A 356 PHE 0.025 0.001 PHE A 344 TRP 0.009 0.001 TRP A 575 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10427) covalent geometry : angle 0.64897 / 0.31 (14204) hydrogen bonds : bond 0.03732 / 2.34 ( 308) hydrogen bonds : angle 4.78892 / 3.16 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.5982 (tmm) REVERT: A 42 MET cc_start: 0.7804 (ttm) cc_final: 0.7505 (ttt) REVERT: A 65 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6705 (mmp) REVERT: A 162 LYS cc_start: 0.6876 (mttt) cc_final: 0.5966 (mmtt) REVERT: A 380 TYR cc_start: 0.4737 (m-80) cc_final: 0.3501 (t80) REVERT: A 498 LYS cc_start: 0.7755 (pptt) cc_final: 0.6651 (tptm) REVERT: A 921 LYS cc_start: 0.6170 (ttpt) cc_final: 0.5948 (mttt) REVERT: A 1115 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7707 (mmt90) REVERT: A 1208 LEU cc_start: 0.7195 (tt) cc_final: 0.6913 (tp) outliers start: 40 outliers final: 20 residues processed: 140 average time/residue: 0.0951 time to fit residues: 19.5920 Evaluate side-chains 118 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 269 GLN A 526 ASN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.186257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.182169 restraints weight = 12618.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.181716 restraints weight = 21239.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.181143 restraints weight = 20441.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.179967 restraints weight = 24481.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.179540 restraints weight = 23033.330| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10427 Z= 0.177 Angle : 0.738 12.175 14204 Z= 0.348 Chirality : 0.055 0.460 1564 Planarity : 0.004 0.076 1754 Dihedral : 11.724 143.837 1622 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.54 % Allowed : 18.16 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.52 (0.23), residues: 1187 helix: -0.67 (0.24), residues: 443 sheet: -2.15 (0.48), residues: 123 loop : -2.37 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.030 0.002 TYR A 356 PHE 0.020 0.002 PHE A 344 TRP 0.011 0.002 TRP A 575 HIS 0.005 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (10427) covalent geometry : angle 0.73809 / 0.35 (14204) hydrogen bonds : bond 0.03969 / 2.65 ( 308) hydrogen bonds : angle 5.01804 / 3.29 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7945 (ttm) cc_final: 0.7689 (ttt) REVERT: A 162 LYS cc_start: 0.6936 (mttt) cc_final: 0.6076 (mmtt) REVERT: A 328 ARG cc_start: 0.4771 (mmm160) cc_final: 0.4392 (mtp-110) REVERT: A 380 TYR cc_start: 0.5038 (m-80) cc_final: 0.3681 (t80) REVERT: A 451 LEU cc_start: 0.2704 (OUTLIER) cc_final: 0.2017 (mt) REVERT: A 498 LYS cc_start: 0.7697 (pptt) cc_final: 0.6875 (mmtp) REVERT: A 1208 LEU cc_start: 0.7373 (tt) cc_final: 0.7094 (tp) outliers start: 45 outliers final: 31 residues processed: 138 average time/residue: 0.0954 time to fit residues: 19.4292 Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.184693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.180432 restraints weight = 12641.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.177435 restraints weight = 20748.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.175742 restraints weight = 29095.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.174446 restraints weight = 20881.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.173148 restraints weight = 20730.055| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10427 Z= 0.210 Angle : 0.775 11.732 14204 Z= 0.367 Chirality : 0.057 0.469 1564 Planarity : 0.004 0.079 1754 Dihedral : 11.841 142.883 1622 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.94 % Allowed : 18.37 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.57 (0.23), residues: 1187 helix: -0.77 (0.24), residues: 441 sheet: -2.17 (0.50), residues: 117 loop : -2.35 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 17 TYR 0.021 0.002 TYR A1116 PHE 0.022 0.002 PHE A 344 TRP 0.014 0.002 TRP A 933 HIS 0.007 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (10427) covalent geometry : angle 0.77537 / 0.37 (14204) hydrogen bonds : bond 0.04164 / 2.79 ( 308) hydrogen bonds : angle 5.17891 / 3.39 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8071 (ttm) cc_final: 0.7811 (ttt) REVERT: A 328 ARG cc_start: 0.4901 (mmm160) cc_final: 0.4518 (mtp-110) REVERT: A 1208 LEU cc_start: 0.7356 (tt) cc_final: 0.7116 (tp) outliers start: 49 outliers final: 36 residues processed: 135 average time/residue: 0.0905 time to fit residues: 18.3618 Evaluate side-chains 128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 276 ASN A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.191310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.187525 restraints weight = 12372.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.185588 restraints weight = 18694.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.184747 restraints weight = 23523.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.182535 restraints weight = 19851.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.180294 restraints weight = 26232.232| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10427 Z= 0.114 Angle : 0.645 10.907 14204 Z= 0.306 Chirality : 0.048 0.395 1564 Planarity : 0.003 0.039 1754 Dihedral : 11.696 146.680 1622 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.33 % Allowed : 20.48 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.25 (0.23), residues: 1187 helix: -0.38 (0.25), residues: 445 sheet: -1.92 (0.50), residues: 122 loop : -2.30 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.014 0.001 TYR A 121 PHE 0.018 0.001 PHE A 344 TRP 0.013 0.001 TRP A 575 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10427) covalent geometry : angle 0.64499 / 0.31 (14204) hydrogen bonds : bond 0.03450 / 2.17 ( 308) hydrogen bonds : angle 4.64529 / 3.04 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6048 (tmm) REVERT: A 42 MET cc_start: 0.7894 (ttm) cc_final: 0.7604 (ttt) REVERT: A 1208 LEU cc_start: 0.7255 (tt) cc_final: 0.7004 (tp) outliers start: 33 outliers final: 24 residues processed: 130 average time/residue: 0.0966 time to fit residues: 18.7285 Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 269 GLN A 276 ASN A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.190155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.189278 restraints weight = 12392.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.175297 restraints weight = 21434.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.174881 restraints weight = 20039.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.174749 restraints weight = 18712.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.174660 restraints weight = 18497.812| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10427 Z= 0.150 Angle : 0.688 11.906 14204 Z= 0.326 Chirality : 0.052 0.424 1564 Planarity : 0.003 0.042 1754 Dihedral : 11.663 143.847 1622 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.34 % Allowed : 20.28 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.12 (0.24), residues: 1187 helix: -0.27 (0.26), residues: 434 sheet: -1.90 (0.50), residues: 122 loop : -2.19 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.013 0.001 TYR A1116 PHE 0.018 0.001 PHE A 344 TRP 0.013 0.002 TRP A1042 HIS 0.011 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10427) covalent geometry : angle 0.68760 / 0.33 (14204) hydrogen bonds : bond 0.03600 / 2.34 ( 308) hydrogen bonds : angle 4.70816 / 3.08 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.7967 (ttm) cc_final: 0.7686 (ttt) REVERT: A 328 ARG cc_start: 0.4559 (tpp80) cc_final: 0.4138 (mtp180) REVERT: A 1208 LEU cc_start: 0.7317 (tt) cc_final: 0.7069 (tp) outliers start: 43 outliers final: 35 residues processed: 135 average time/residue: 0.0874 time to fit residues: 17.8952 Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 276 ASN A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.188058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.186736 restraints weight = 12475.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.186432 restraints weight = 20961.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.186182 restraints weight = 25129.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.171660 restraints weight = 25914.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.168759 restraints weight = 34776.856| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10427 Z= 0.163 Angle : 0.715 12.792 14204 Z= 0.340 Chirality : 0.052 0.386 1564 Planarity : 0.004 0.044 1754 Dihedral : 11.737 143.820 1622 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 4.34 % Allowed : 20.28 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.16 (0.24), residues: 1187 helix: -0.29 (0.26), residues: 434 sheet: -1.96 (0.50), residues: 122 loop : -2.20 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.015 0.001 TYR A 189 PHE 0.018 0.001 PHE A 344 TRP 0.025 0.002 TRP A1042 HIS 0.009 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (10427) covalent geometry : angle 0.71545 / 0.34 (14204) hydrogen bonds : bond 0.03697 / 2.43 ( 308) hydrogen bonds : angle 4.79004 / 3.13 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.7936 (ttm) cc_final: 0.7662 (ttt) REVERT: A 162 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7546 (mtmm) REVERT: A 328 ARG cc_start: 0.4889 (tpp80) cc_final: 0.4342 (mtp180) REVERT: A 1208 LEU cc_start: 0.7419 (tt) cc_final: 0.7149 (tp) outliers start: 43 outliers final: 39 residues processed: 129 average time/residue: 0.0947 time to fit residues: 18.1594 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.185323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3800 r_free = 0.3800 target = 0.172369 restraints weight = 12417.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.171991 restraints weight = 18116.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.171909 restraints weight = 16352.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.171908 restraints weight = 15828.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.171908 restraints weight = 13494.498| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10427 Z= 0.195 Angle : 0.756 12.850 14204 Z= 0.358 Chirality : 0.056 0.440 1564 Planarity : 0.004 0.050 1754 Dihedral : 11.888 143.218 1622 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.64 % Allowed : 20.38 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.31 (0.23), residues: 1187 helix: -0.51 (0.25), residues: 440 sheet: -1.89 (0.51), residues: 119 loop : -2.27 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.018 0.002 TYR A1116 PHE 0.018 0.002 PHE A 344 TRP 0.031 0.003 TRP A1042 HIS 0.008 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (10427) covalent geometry : angle 0.75623 / 0.36 (14204) hydrogen bonds : bond 0.03948 / 2.64 ( 308) hydrogen bonds : angle 4.93639 / 3.22 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.7972 (ttm) cc_final: 0.7718 (ttt) REVERT: A 162 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7726 (mtmm) REVERT: A 1208 LEU cc_start: 0.7415 (tt) cc_final: 0.7161 (tp) outliers start: 46 outliers final: 41 residues processed: 128 average time/residue: 0.0973 time to fit residues: 18.3714 Evaluate side-chains 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 526 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.184198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.182605 restraints weight = 12554.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.166235 restraints weight = 22985.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.165276 restraints weight = 22597.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.164335 restraints weight = 22542.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.164630 restraints weight = 19708.470| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10427 Z= 0.208 Angle : 0.781 12.737 14204 Z= 0.369 Chirality : 0.056 0.432 1564 Planarity : 0.004 0.054 1754 Dihedral : 11.943 143.312 1622 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.64 % Allowed : 20.59 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.37 (0.23), residues: 1187 helix: -0.61 (0.25), residues: 444 sheet: -2.11 (0.53), residues: 111 loop : -2.23 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 474 TYR 0.019 0.002 TYR A1116 PHE 0.019 0.002 PHE A 344 TRP 0.037 0.003 TRP A1042 HIS 0.008 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (10427) covalent geometry : angle 0.78072 / 0.37 (14204) hydrogen bonds : bond 0.04082 / 2.73 ( 308) hydrogen bonds : angle 5.04771 / 3.29 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.88 seconds wall clock time: 28 minutes 25.36 seconds (1705.36 seconds total)