Starting phenix.real_space_refine on Mon Jul 28 14:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_9742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_9742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_9742.map" model { file = "/net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_9742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iv6_9742/07_2025/6iv6_9742.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'ARG:plan': 3, 'ALY:plan-2': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 178 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 547 Classifications: {'RNA': 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: 7.29, per 1000 atoms: 0.72 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.32 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: 4.32 Time building geometry restraints manager: 3.09 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: 13919 3.08 - 6.17: 241 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 - 35.87: 6061 35.87 - 71.73: 183 71.73 - 107.60: 17 107.60 - 143.47: 1 143.47 - 179.33: 3 Dihedral angle restraints: 6265 sinusoidal: 2725 harmonic: 3540 Sorted by residual: dihedral pdb=" O4' C G 23 " pdb=" C1' C G 23 " pdb=" N1 C G 23 " pdb=" C2 C G 23 " ideal model delta sinusoidal sigma weight residual 200.00 51.91 148.09 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 52.67 179.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 15 " pdb=" C1' U G 15 " pdb=" N1 U G 15 " pdb=" C2 U G 15 " ideal model delta sinusoidal sigma weight residual -128.00 48.81 -176.81 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 6262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1338 0.074 - 0.148: 199 0.148 - 0.223: 21 0.223 - 0.297: 5 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=" CA ASP A 665 " pdb=" N ASP A 665 " pdb=" C ASP A 665 " pdb=" CB ASP A 665 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB THR A 516 " pdb=" CA THR A 516 " pdb=" OG1 THR A 516 " pdb=" CG2 THR A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+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: 1.180 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.300 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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= 0.280 Angle : 1.041 15.413 14204 Z= 0.578 Chirality : 0.053 0.371 1564 Planarity : 0.008 0.155 1754 Dihedral : 17.648 179.332 3987 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP A1042 HIS 0.006 0.001 HIS A 193 PHE 0.020 0.002 PHE A 18 TYR 0.034 0.002 TYR A 327 ARG 0.007 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.27162 ( 308) hydrogen bonds : angle 10.00735 ( 867) covalent geometry : bond 0.00537 (10427) covalent geometry : angle 1.04073 (14204) *********************** 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 : 1.111 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: 0.5649 (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: 0.6786 (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: 0.6663 (t70) REVERT: A 1115 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7252 (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: 0.2534 time to fit residues: 59.0223 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 : 1.077 ------------------------------------------------------------------------------- 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 103 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 159 HIS A 204 GLN A 219 GLN A 236 HIS A 269 GLN A 279 HIS A 296 HIS A 506 ASN A 526 ASN A 612 ASN A 619 GLN 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 910 GLN A1018 GLN A1043 ASN A1089 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.181745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.177564 restraints weight = 12591.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.174934 restraints weight = 21216.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.172640 restraints weight = 28009.101| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10427 Z= 0.259 Angle : 0.776 12.028 14204 Z= 0.396 Chirality : 0.047 0.202 1564 Planarity : 0.005 0.048 1754 Dihedral : 15.238 174.213 1714 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.85 % Favored : 91.07 % Rotamer: Outliers : 3.43 % Allowed : 15.14 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.19), residues: 1187 helix: -2.61 (0.18), residues: 424 sheet: -2.62 (0.46), residues: 117 loop : -2.73 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1106 HIS 0.012 0.002 HIS A 509 PHE 0.021 0.002 PHE A 18 TYR 0.023 0.002 TYR A 327 ARG 0.008 0.001 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 308) hydrogen bonds : angle 6.11957 ( 867) covalent geometry : bond 0.00606 (10427) covalent geometry : angle 0.77554 (14204) *********************** 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 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.8065 (ttm) cc_final: 0.7836 (ttt) REVERT: A 162 LYS cc_start: 0.7022 (mttt) cc_final: 0.6031 (mmtt) REVERT: A 328 ARG cc_start: 0.5072 (mmm160) cc_final: 0.4821 (mtp180) REVERT: A 380 TYR cc_start: 0.4900 (m-80) cc_final: 0.3973 (t80) REVERT: A 460 LYS cc_start: 0.5423 (mmtp) cc_final: 0.5049 (mmtp) REVERT: A 498 LYS cc_start: 0.7991 (pptt) cc_final: 0.7042 (tptm) REVERT: A 921 LYS cc_start: 0.6624 (ttpt) cc_final: 0.6252 (mttt) REVERT: A 935 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6451 (mp0) REVERT: A 1115 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7707 (mmt90) REVERT: A 1208 LEU cc_start: 0.7031 (tt) cc_final: 0.6726 (tp) outliers start: 34 outliers final: 17 residues processed: 136 average time/residue: 0.2319 time to fit residues: 44.5990 Evaluate side-chains 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 376 VAL 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 722 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.0020 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 269 GLN A 459 GLN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS A 869 ASN A1198 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.190307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.185464 restraints weight = 12535.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.174720 restraints weight = 24471.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.172051 restraints weight = 26282.684| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10427 Z= 0.114 Angle : 0.596 10.348 14204 Z= 0.301 Chirality : 0.041 0.194 1564 Planarity : 0.004 0.038 1754 Dihedral : 14.876 177.963 1712 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.33 % Allowed : 18.37 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.21), residues: 1187 helix: -1.37 (0.23), residues: 435 sheet: -2.62 (0.45), residues: 125 loop : -2.56 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.004 0.001 HIS A 509 PHE 0.014 0.001 PHE A 18 TYR 0.024 0.001 TYR A 121 ARG 0.005 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 308) hydrogen bonds : angle 5.25695 ( 867) covalent geometry : bond 0.00249 (10427) covalent geometry : angle 0.59627 (14204) *********************** 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 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.046 Fit side-chains REVERT: A 1 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6006 (tmm) REVERT: A 42 MET cc_start: 0.7891 (ttm) cc_final: 0.7617 (ttt) REVERT: A 162 LYS cc_start: 0.6857 (mttt) cc_final: 0.5908 (mmtt) REVERT: A 328 ARG cc_start: 0.5067 (mmm160) cc_final: 0.4761 (mtp180) REVERT: A 362 LEU cc_start: 0.7788 (tt) cc_final: 0.7523 (tp) REVERT: A 380 TYR cc_start: 0.4756 (m-80) cc_final: 0.3474 (t80) REVERT: A 460 LYS cc_start: 0.5125 (mmtp) cc_final: 0.4744 (mmtp) REVERT: A 498 LYS cc_start: 0.7876 (pptt) cc_final: 0.6562 (mmmm) REVERT: A 921 LYS cc_start: 0.6175 (ttpt) cc_final: 0.5881 (mttt) REVERT: A 1113 ASP cc_start: 0.6699 (t70) cc_final: 0.6451 (t70) REVERT: A 1115 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7646 (mmt90) REVERT: A 1208 LEU cc_start: 0.7200 (tt) cc_final: 0.6917 (tp) outliers start: 33 outliers final: 15 residues processed: 140 average time/residue: 0.2321 time to fit residues: 45.8431 Evaluate side-chains 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 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 919 LEU 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 119 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 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 = 0.3879 r_free = 0.3879 target = 0.178724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.174768 restraints weight = 12634.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.174253 restraints weight = 18874.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173519 restraints weight = 20519.633| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10427 Z= 0.280 Angle : 0.769 11.326 14204 Z= 0.390 Chirality : 0.049 0.202 1564 Planarity : 0.005 0.093 1754 Dihedral : 15.189 172.465 1712 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.86 % Favored : 90.06 % Rotamer: Outliers : 5.65 % Allowed : 18.26 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.22), residues: 1187 helix: -1.44 (0.23), residues: 444 sheet: -2.52 (0.47), residues: 124 loop : -2.57 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 689 HIS 0.006 0.001 HIS A 759 PHE 0.032 0.002 PHE A 344 TYR 0.024 0.002 TYR A1116 ARG 0.003 0.001 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 308) hydrogen bonds : angle 5.73940 ( 867) covalent geometry : bond 0.00651 (10427) covalent geometry : angle 0.76870 (14204) *********************** 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 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8103 (ttm) cc_final: 0.7897 (ttt) REVERT: A 328 ARG cc_start: 0.5103 (mmm160) cc_final: 0.4891 (mtp180) REVERT: A 498 LYS cc_start: 0.7857 (pptt) cc_final: 0.7123 (mmtp) REVERT: A 1115 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7795 (mmt90) REVERT: A 1208 LEU cc_start: 0.7454 (tt) cc_final: 0.7191 (tp) outliers start: 56 outliers final: 35 residues processed: 144 average time/residue: 0.2164 time to fit residues: 44.8653 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 232 SER Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 274 LEU 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 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 738 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 806 LEU 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 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1054 VAL 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 1227 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.188497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.184201 restraints weight = 12332.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.183287 restraints weight = 20631.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.182355 restraints weight = 22375.721| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3885 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= 0.118 Angle : 0.597 11.074 14204 Z= 0.299 Chirality : 0.041 0.190 1564 Planarity : 0.003 0.051 1754 Dihedral : 14.876 176.992 1712 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.94 % Allowed : 20.28 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.23), residues: 1187 helix: -0.83 (0.24), residues: 447 sheet: -2.41 (0.48), residues: 122 loop : -2.48 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.004 0.001 HIS A 156 PHE 0.023 0.001 PHE A 344 TYR 0.017 0.001 TYR A 121 ARG 0.004 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 308) hydrogen bonds : angle 5.03491 ( 867) covalent geometry : bond 0.00261 (10427) covalent geometry : angle 0.59749 (14204) *********************** 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 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7985 (ttm) cc_final: 0.7706 (ttt) REVERT: A 495 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5927 (tmm160) REVERT: A 498 LYS cc_start: 0.7752 (pptt) cc_final: 0.6549 (mmmm) REVERT: A 1115 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7762 (mmt90) REVERT: A 1208 LEU cc_start: 0.7299 (tt) cc_final: 0.7029 (tp) outliers start: 39 outliers final: 25 residues processed: 136 average time/residue: 0.2426 time to fit residues: 47.6941 Evaluate side-chains 119 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 209 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 587 ILE 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 724 ILE Chi-restraints excluded: chain A residue 738 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 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3939 r_free = 0.3939 target = 0.185537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.180812 restraints weight = 12556.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.168314 restraints weight = 20970.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.166287 restraints weight = 22443.107| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10427 Z= 0.183 Angle : 0.656 11.734 14204 Z= 0.329 Chirality : 0.044 0.191 1564 Planarity : 0.004 0.055 1754 Dihedral : 14.916 173.502 1712 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 5.15 % Allowed : 20.18 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1187 helix: -0.75 (0.24), residues: 440 sheet: -2.34 (0.48), residues: 122 loop : -2.40 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.008 0.001 HIS A 509 PHE 0.022 0.002 PHE A 344 TYR 0.016 0.002 TYR A1116 ARG 0.007 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 308) hydrogen bonds : angle 5.14221 ( 867) covalent geometry : bond 0.00427 (10427) covalent geometry : angle 0.65642 (14204) *********************** 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 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 96 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8009 (ttm) cc_final: 0.7730 (ttt) REVERT: A 495 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6053 (tmm160) REVERT: A 1115 ARG cc_start: 0.8198 (mmt180) cc_final: 0.7896 (mmt90) REVERT: A 1208 LEU cc_start: 0.7499 (tt) cc_final: 0.7229 (tp) outliers start: 51 outliers final: 40 residues processed: 138 average time/residue: 0.2192 time to fit residues: 42.9462 Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 587 ILE 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 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 868 VAL 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 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1001 VAL 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 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 52 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 526 ASN ** A 686 HIS ** 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 = 0.3945 r_free = 0.3945 target = 0.186020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.182070 restraints weight = 12626.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.181171 restraints weight = 19589.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.180467 restraints weight = 23545.518| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10427 Z= 0.142 Angle : 0.610 11.197 14204 Z= 0.306 Chirality : 0.042 0.192 1564 Planarity : 0.004 0.042 1754 Dihedral : 14.804 175.456 1712 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.35 % Allowed : 20.18 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1187 helix: -0.59 (0.25), residues: 438 sheet: -2.22 (0.49), residues: 122 loop : -2.35 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 575 HIS 0.006 0.001 HIS A 509 PHE 0.020 0.001 PHE A 344 TYR 0.015 0.001 TYR A 121 ARG 0.006 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 308) hydrogen bonds : angle 4.93076 ( 867) covalent geometry : bond 0.00327 (10427) covalent geometry : angle 0.61044 (14204) *********************** 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 151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7996 (ttm) cc_final: 0.7748 (ttt) REVERT: A 328 ARG cc_start: 0.4601 (tpp80) cc_final: 0.4230 (mtp180) REVERT: A 495 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.6064 (tmm160) REVERT: A 498 LYS cc_start: 0.7522 (pptt) cc_final: 0.6589 (mmtp) REVERT: A 1115 ARG cc_start: 0.8006 (mmt180) cc_final: 0.7772 (mmt90) REVERT: A 1208 LEU cc_start: 0.7359 (tt) cc_final: 0.7078 (tp) outliers start: 53 outliers final: 42 residues processed: 141 average time/residue: 0.2199 time to fit residues: 45.4098 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 65 MET 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 249 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 587 ILE 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 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 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1001 VAL 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 1227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 0.0060 chunk 79 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 ASN A 526 ASN A 686 HIS A 949 HIS A1043 ASN A1251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.192162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.188004 restraints weight = 12442.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.187227 restraints weight = 18424.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.186560 restraints weight = 20857.329| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10427 Z= 0.104 Angle : 0.565 10.628 14204 Z= 0.283 Chirality : 0.040 0.185 1564 Planarity : 0.003 0.032 1754 Dihedral : 14.585 179.020 1712 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.14 % Allowed : 21.29 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1187 helix: -0.21 (0.26), residues: 434 sheet: -1.98 (0.49), residues: 122 loop : -2.24 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 575 HIS 0.009 0.001 HIS A 509 PHE 0.019 0.001 PHE A 344 TYR 0.014 0.001 TYR A 121 ARG 0.005 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 308) hydrogen bonds : angle 4.60174 ( 867) covalent geometry : bond 0.00230 (10427) covalent geometry : angle 0.56495 (14204) *********************** 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 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.5745 (tmm) REVERT: A 42 MET cc_start: 0.7870 (ttm) cc_final: 0.7630 (ttt) REVERT: A 86 ASN cc_start: 0.4711 (t0) cc_final: 0.4473 (t0) REVERT: A 328 ARG cc_start: 0.4534 (tpp80) cc_final: 0.4210 (mtp180) REVERT: A 498 LYS cc_start: 0.7500 (pptt) cc_final: 0.6560 (mmtp) REVERT: A 1115 ARG cc_start: 0.7920 (mmt180) cc_final: 0.7718 (mmt90) REVERT: A 1208 LEU cc_start: 0.7314 (tt) cc_final: 0.7021 (tp) outliers start: 41 outliers final: 26 residues processed: 140 average time/residue: 0.2086 time to fit residues: 42.4004 Evaluate side-chains 124 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 249 ILE 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 643 LEU 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 902 THR Chi-restraints excluded: chain A residue 909 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 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 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 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 = 0.3959 r_free = 0.3959 target = 0.187539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.186093 restraints weight = 12562.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.172059 restraints weight = 21123.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.169462 restraints weight = 29287.183| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10427 Z= 0.134 Angle : 0.601 13.168 14204 Z= 0.299 Chirality : 0.042 0.296 1564 Planarity : 0.004 0.047 1754 Dihedral : 14.568 175.797 1712 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.24 % Allowed : 21.49 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1187 helix: -0.23 (0.26), residues: 438 sheet: -1.95 (0.49), residues: 122 loop : -2.19 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 575 HIS 0.007 0.001 HIS A 509 PHE 0.018 0.001 PHE A 344 TYR 0.014 0.001 TYR A 121 ARG 0.005 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 308) hydrogen bonds : angle 4.64270 ( 867) covalent geometry : bond 0.00309 (10427) covalent geometry : angle 0.60141 (14204) *********************** 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 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6187 (tmm) REVERT: A 42 MET cc_start: 0.7893 (ttm) cc_final: 0.7629 (ttt) REVERT: A 86 ASN cc_start: 0.4510 (t0) cc_final: 0.4304 (t0) REVERT: A 328 ARG cc_start: 0.4680 (tpp80) cc_final: 0.4221 (mtp180) REVERT: A 498 LYS cc_start: 0.7687 (pptt) cc_final: 0.6467 (tppp) REVERT: A 1115 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7850 (mmt90) REVERT: A 1208 LEU cc_start: 0.7442 (tt) cc_final: 0.7160 (tp) outliers start: 42 outliers final: 34 residues processed: 129 average time/residue: 0.2162 time to fit residues: 41.0630 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 587 ILE 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 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 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 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 1015 ASN 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 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 25 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.0010 chunk 47 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 ASN A 526 ASN ** A 686 HIS ** 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 = 0.3979 r_free = 0.3979 target = 0.189685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.185464 restraints weight = 12393.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.184638 restraints weight = 22339.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.184221 restraints weight = 22823.376| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10427 Z= 0.130 Angle : 0.606 12.883 14204 Z= 0.300 Chirality : 0.042 0.287 1564 Planarity : 0.003 0.035 1754 Dihedral : 14.540 175.603 1712 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.63 % Allowed : 22.30 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1187 helix: -0.11 (0.26), residues: 432 sheet: -1.92 (0.49), residues: 122 loop : -2.15 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 575 HIS 0.007 0.001 HIS A 509 PHE 0.018 0.001 PHE A 344 TYR 0.013 0.001 TYR A 121 ARG 0.005 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 308) hydrogen bonds : angle 4.61169 ( 867) covalent geometry : bond 0.00300 (10427) covalent geometry : angle 0.60635 (14204) ********************** 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 128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6151 (tmm) REVERT: A 42 MET cc_start: 0.7966 (ttm) cc_final: 0.7709 (ttt) REVERT: A 328 ARG cc_start: 0.4509 (tpp80) cc_final: 0.4196 (mtp180) REVERT: A 1208 LEU cc_start: 0.7361 (tt) cc_final: 0.7101 (tp) outliers start: 36 outliers final: 31 residues processed: 122 average time/residue: 0.2073 time to fit residues: 37.1274 Evaluate side-chains 119 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 587 ILE 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 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 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1015 ASN 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 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 68 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 276 ASN A 428 HIS A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3908 r_free = 0.3908 target = 0.182024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.180830 restraints weight = 12591.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.163842 restraints weight = 21188.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.162699 restraints weight = 27524.817| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10427 Z= 0.258 Angle : 0.740 13.020 14204 Z= 0.369 Chirality : 0.048 0.292 1564 Planarity : 0.004 0.045 1754 Dihedral : 14.867 171.338 1712 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 4.64 % Allowed : 21.19 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1187 helix: -0.67 (0.25), residues: 440 sheet: -2.15 (0.49), residues: 117 loop : -2.37 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1254 HIS 0.008 0.002 HIS A 916 PHE 0.020 0.002 PHE A 471 TYR 0.021 0.002 TYR A1116 ARG 0.006 0.001 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 308) hydrogen bonds : angle 5.17372 ( 867) covalent geometry : bond 0.00604 (10427) covalent geometry : angle 0.73957 (14204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.31 seconds wall clock time: 54 minutes 25.92 seconds (3265.92 seconds total)