Starting phenix.real_space_refine on Sat Sep 12 01:12:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.map" model { file = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nma_0445/09_2026/6nma_0445.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 7870 2.51 5 N 2049 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12404 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "B" Number of atoms: 9974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9974 Classifications: {'peptide': 1206} Link IDs: {'PTRANS': 25, 'TRANS': 1180} Chain breaks: 4 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 942 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.21 Number of scatterers: 12404 At special positions: 0 Unit cell: (126.854, 108.732, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 25 15.00 Mg 2 11.99 O 2417 8.00 N 2049 7.00 C 7870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 370.7 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 45.4% alpha, 9.7% beta 6 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 120 through 125 removed outlier: 4.091A pdb=" N VAL A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 125' Processing helix chain 'A' and resid 126 through 129 removed outlier: 5.018A pdb=" N ARG A 129 " --> pdb=" O ALA A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.715A pdb=" N LYS A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.636A pdb=" N ARG A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.688A pdb=" N ASN B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 66 removed outlier: 3.638A pdb=" N ALA B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLY B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 4.385A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.984A pdb=" N LEU B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.644A pdb=" N GLU B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.889A pdb=" N GLU B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 removed outlier: 4.038A pdb=" N VAL B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.645A pdb=" N VAL B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.779A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.522A pdb=" N ILE B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 341 through 351 removed outlier: 4.134A pdb=" N SER B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.561A pdb=" N ASP B 360 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.809A pdb=" N PHE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 437' Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.721A pdb=" N SER B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.738A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.597A pdb=" N ARG B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 588 through 598 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 629 through 644 removed outlier: 4.005A pdb=" N HIS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 718 through 727 removed outlier: 3.516A pdb=" N MET B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.941A pdb=" N ARG B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.808A pdb=" N GLU B 885 " --> pdb=" O LYS B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 900 Processing helix chain 'B' and resid 907 through 919 removed outlier: 3.813A pdb=" N LEU B 914 " --> pdb=" O LYS B 910 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 916 " --> pdb=" O CYS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 930 removed outlier: 4.265A pdb=" N GLY B 930 " --> pdb=" O LEU B 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 930' Processing helix chain 'B' and resid 939 through 948 removed outlier: 3.819A pdb=" N LYS B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 955 Processing helix chain 'B' and resid 1020 through 1031 removed outlier: 3.645A pdb=" N SER B1024 " --> pdb=" O SER B1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 removed outlier: 3.597A pdb=" N TYR B1102 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1120 through 1135 removed outlier: 4.468A pdb=" N TYR B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B1128 " --> pdb=" O TYR B1124 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B1129 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B1135 " --> pdb=" O MET B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1167 Processing helix chain 'B' and resid 1180 through 1199 removed outlier: 3.671A pdb=" N LYS B1190 " --> pdb=" O ASN B1186 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B1191 " --> pdb=" O ILE B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1209 Processing helix chain 'B' and resid 1214 through 1225 Processing helix chain 'C' and resid 123 through 149 removed outlier: 3.733A pdb=" N ALA C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.980A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.589A pdb=" N VAL A 207 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.168A pdb=" N TYR B 794 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.666A pdb=" N ARG B 737 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA6, first strand: chain 'B' and resid 552 through 556 removed outlier: 4.923A pdb=" N ILE B 546 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 581 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 758 through 759 removed outlier: 3.551A pdb=" N VAL B 783 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 850 through 855 removed outlier: 3.539A pdb=" N GLU B 852 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU B 925 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 922 " --> pdb=" O PHE B 994 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 996 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 924 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 858 through 863 Processing sheet with id=AB1, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.544A pdb=" N LEU B1042 " --> pdb=" O VAL B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1070 through 1073 Processing sheet with id=AB3, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.467A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2341 1.32 - 1.44: 3250 1.44 - 1.57: 7003 1.57 - 1.69: 49 1.69 - 1.81: 67 Bond restraints: 12710 Sorted by residual: bond pdb=" N SER B 855 " pdb=" CA SER B 855 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N GLU B 882 " pdb=" CA GLU B 882 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.65e+00 bond pdb=" CA GLN B 975 " pdb=" CB GLN B 975 " ideal model delta sigma weight residual 1.527 1.459 0.068 2.48e-02 1.63e+03 7.48e+00 bond pdb=" N LEU B 856 " pdb=" CA LEU B 856 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N ARG B1112 " pdb=" CA ARG B1112 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.64e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16194 1.56 - 3.13: 874 3.13 - 4.69: 114 4.69 - 6.25: 34 6.25 - 7.82: 8 Bond angle restraints: 17224 Sorted by residual: angle pdb=" N ILE B 904 " pdb=" CA ILE B 904 " pdb=" C ILE B 904 " ideal model delta sigma weight residual 111.91 107.11 4.80 8.90e-01 1.26e+00 2.91e+01 angle pdb=" N ILE B1141 " pdb=" CA ILE B1141 " pdb=" C ILE B1141 " ideal model delta sigma weight residual 113.53 109.79 3.74 9.80e-01 1.04e+00 1.45e+01 angle pdb=" C ASN C 169 " pdb=" N LEU C 170 " pdb=" CA LEU C 170 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N GLY B 902 " pdb=" CA GLY B 902 " pdb=" C GLY B 902 " ideal model delta sigma weight residual 113.18 105.36 7.82 2.37e+00 1.78e-01 1.09e+01 angle pdb=" N ILE B1111 " pdb=" CA ILE B1111 " pdb=" C ILE B1111 " ideal model delta sigma weight residual 111.91 109.04 2.87 8.90e-01 1.26e+00 1.04e+01 ... (remaining 17219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6786 17.83 - 35.65: 639 35.65 - 53.48: 153 53.48 - 71.31: 65 71.31 - 89.13: 23 Dihedral angle restraints: 7666 sinusoidal: 3399 harmonic: 4267 Sorted by residual: dihedral pdb=" C4' U G 12 " pdb=" C3' U G 12 " pdb=" C2' U G 12 " pdb=" C1' U G 12 " ideal model delta sinusoidal sigma weight residual 36.34 -39.77 76.12 1 3.10e+00 1.04e-01 7.59e+02 dihedral pdb=" C4' U G 5 " pdb=" C3' U G 5 " pdb=" C2' U G 5 " pdb=" C1' U G 5 " ideal model delta sinusoidal sigma weight residual 36.34 -38.75 75.09 1 3.10e+00 1.04e-01 7.42e+02 dihedral pdb=" C4' U G 16 " pdb=" C3' U G 16 " pdb=" C2' U G 16 " pdb=" C1' U G 16 " ideal model delta sinusoidal sigma weight residual 36.35 -37.16 73.50 1 3.10e+00 1.04e-01 7.15e+02 ... (remaining 7663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1458 0.062 - 0.124: 348 0.124 - 0.186: 25 0.186 - 0.247: 21 0.247 - 0.309: 13 Chirality restraints: 1865 Sorted by residual: chirality pdb=" C2' U G 12 " pdb=" C3' U G 12 " pdb=" O2' U G 12 " pdb=" C1' U G 12 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C2' A G 3 " pdb=" C3' A G 3 " pdb=" O2' A G 3 " pdb=" C1' A G 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' U G 16 " pdb=" C4' U G 16 " pdb=" O3' U G 16 " pdb=" C2' U G 16 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1862 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C G 11 " 0.027 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 C G 11 " -0.037 2.00e-02 2.50e+03 pdb=" C2 C G 11 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C G 11 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C G 11 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C G 11 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C G 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 21 " -0.029 2.00e-02 2.50e+03 1.23e-02 4.17e+00 pdb=" N9 A G 21 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A G 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 A G 21 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A G 21 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A G 21 " -0.007 2.00e-02 2.50e+03 pdb=" N6 A G 21 " -0.012 2.00e-02 2.50e+03 pdb=" N1 A G 21 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A G 21 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A G 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A G 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 193 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 194 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 141 2.56 - 3.14: 10455 3.14 - 3.73: 18256 3.73 - 4.31: 26135 4.31 - 4.90: 42863 Nonbonded interactions: 97850 Sorted by model distance: nonbonded pdb=" NZ LYS A 202 " pdb="MG MG A 301 " model vdw 1.973 2.250 nonbonded pdb=" OP2 A G 19 " pdb="MG MG G1301 " model vdw 2.020 2.170 nonbonded pdb=" O THR B1055 " pdb=" OG1 THR B1055 " model vdw 2.104 3.040 nonbonded pdb=" O THR B 246 " pdb=" OG1 THR B 246 " model vdw 2.197 3.040 nonbonded pdb=" O LYS B 595 " pdb=" OG SER B 599 " model vdw 2.200 3.040 ... (remaining 97845 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 120 through 233) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.009 0.078 12710 Z= 0.413 Angle : 0.824 7.816 17224 Z= 0.463 Chirality : 0.059 0.309 1865 Planarity : 0.004 0.049 2110 Dihedral : 16.203 89.134 4914 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.98 % Favored : 88.95 % Rotamer: Outliers : 8.09 % Allowed : 10.46 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.17), residues: 1421 helix: -2.79 (0.16), residues: 586 sheet: -3.82 (0.33), residues: 163 loop : -3.58 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 747 TYR 0.024 0.002 TYR B 294 PHE 0.017 0.002 PHE B 61 TRP 0.013 0.002 TRP B 534 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.41 (12710) covalent geometry : angle 0.82418 / 0.46 (17224) hydrogen bonds : bond 0.16615 / 10.36 ( 447) hydrogen bonds : angle 7.54168 / 5.12 ( 1258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 212 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8323 (t0) cc_final: 0.8072 (t0) REVERT: A 186 MET cc_start: 0.8848 (mtp) cc_final: 0.8623 (mtp) REVERT: B 26 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7687 (tttm) REVERT: B 142 ASN cc_start: 0.8150 (t0) cc_final: 0.7897 (p0) REVERT: B 227 PHE cc_start: 0.7724 (t80) cc_final: 0.7460 (t80) REVERT: B 244 PHE cc_start: 0.7410 (t80) cc_final: 0.7175 (m-80) REVERT: B 248 SER cc_start: 0.2824 (OUTLIER) cc_final: 0.2473 (p) REVERT: B 319 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8239 (mmtt) REVERT: B 474 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: B 495 ASP cc_start: 0.8369 (t0) cc_final: 0.7968 (t0) REVERT: B 531 MET cc_start: 0.9157 (ttt) cc_final: 0.8782 (mtp) REVERT: B 534 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.8153 (m100) REVERT: B 701 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: B 712 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8569 (mmtp) REVERT: B 752 LYS cc_start: 0.8653 (mptt) cc_final: 0.8217 (mmtt) REVERT: B 864 ASN cc_start: 0.9112 (t0) cc_final: 0.8817 (t0) REVERT: B 882 GLU cc_start: 0.7634 (tp30) cc_final: 0.6961 (tt0) REVERT: B 889 ASN cc_start: 0.7747 (m110) cc_final: 0.6790 (t0) REVERT: B 893 ILE cc_start: 0.8863 (tt) cc_final: 0.8545 (tt) REVERT: B 945 LYS cc_start: 0.8201 (tptm) cc_final: 0.7801 (ttpt) REVERT: B 986 MET cc_start: 0.8858 (mtt) cc_final: 0.8539 (mtt) REVERT: B 999 TRP cc_start: 0.8177 (m-90) cc_final: 0.7650 (m100) REVERT: B 1017 LYS cc_start: 0.8493 (ptmt) cc_final: 0.8184 (pttp) REVERT: B 1035 MET cc_start: 0.7423 (ptt) cc_final: 0.7052 (ptm) REVERT: B 1056 ASP cc_start: 0.8055 (t0) cc_final: 0.7538 (t0) REVERT: B 1085 ASP cc_start: 0.7368 (t0) cc_final: 0.7077 (t70) REVERT: B 1115 LEU cc_start: 0.8927 (mm) cc_final: 0.8513 (mm) REVERT: B 1118 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7472 (mp10) REVERT: B 1131 MET cc_start: 0.8740 (tpp) cc_final: 0.8389 (tpp) REVERT: B 1148 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8194 (t0) REVERT: C 157 ASN cc_start: 0.7763 (m110) cc_final: 0.7482 (m-40) REVERT: C 165 LEU cc_start: 0.8677 (mt) cc_final: 0.8441 (mt) REVERT: C 172 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5540 (pp) REVERT: C 190 HIS cc_start: 0.8388 (p-80) cc_final: 0.8167 (p-80) REVERT: C 232 LEU cc_start: 0.8681 (tp) cc_final: 0.8419 (tt) outliers start: 106 outliers final: 61 residues processed: 298 average time/residue: 0.1111 time to fit residues: 47.6120 Evaluate side-chains 236 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 534 TRP Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 627 PHE Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 712 LYS Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1005 ASP Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1055 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1149 PHE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 208 ASN B 33 ASN B 63 ASN B 157 ASN B 263 ASN B 567 GLN B 651 ASN B 676 GLN B 793 GLN B 797 HIS B 808 ASN B 861 ASN B 889 ASN B 906 GLN ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113485 restraints weight = 15706.422| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.75 r_work: 0.3106 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12710 Z= 0.135 Angle : 0.682 9.904 17224 Z= 0.337 Chirality : 0.057 0.628 1865 Planarity : 0.004 0.040 2110 Dihedral : 13.217 153.523 1991 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.27 % Allowed : 14.58 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.21), residues: 1421 helix: -1.22 (0.20), residues: 595 sheet: -3.54 (0.32), residues: 176 loop : -2.73 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1112 TYR 0.021 0.001 TYR B1036 PHE 0.025 0.001 PHE B 131 TRP 0.008 0.001 TRP B 999 HIS 0.003 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12710) covalent geometry : angle 0.68183 / 0.34 (17224) hydrogen bonds : bond 0.03664 / 2.36 ( 447) hydrogen bonds : angle 5.24676 / 3.50 ( 1258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8257 (tp30) cc_final: 0.8021 (tp30) REVERT: A 178 TRP cc_start: 0.8551 (m100) cc_final: 0.8094 (m100) REVERT: A 180 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8249 (mt-10) REVERT: A 181 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: A 217 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7261 (ptm-80) REVERT: B 26 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7396 (tttm) REVERT: B 45 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7684 (tt0) REVERT: B 221 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: B 319 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8234 (mmtt) REVERT: B 331 TYR cc_start: 0.8158 (m-80) cc_final: 0.7556 (m-80) REVERT: B 433 GLU cc_start: 0.9089 (tp30) cc_final: 0.8772 (tp30) REVERT: B 474 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: B 476 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: B 495 ASP cc_start: 0.8411 (t0) cc_final: 0.8065 (t0) REVERT: B 531 MET cc_start: 0.8922 (ttt) cc_final: 0.8557 (mtp) REVERT: B 562 TYR cc_start: 0.8121 (m-80) cc_final: 0.7835 (m-80) REVERT: B 752 LYS cc_start: 0.8646 (mptt) cc_final: 0.8247 (mmtm) REVERT: B 864 ASN cc_start: 0.9212 (t0) cc_final: 0.8915 (t0) REVERT: B 882 GLU cc_start: 0.7761 (tp30) cc_final: 0.7384 (tt0) REVERT: B 889 ASN cc_start: 0.7500 (m-40) cc_final: 0.6638 (t0) REVERT: B 893 ILE cc_start: 0.8758 (tt) cc_final: 0.8489 (tt) REVERT: B 986 MET cc_start: 0.8832 (mtt) cc_final: 0.8599 (mtt) REVERT: B 1037 VAL cc_start: 0.8415 (m) cc_final: 0.8184 (m) REVERT: B 1056 ASP cc_start: 0.8379 (t0) cc_final: 0.7868 (t0) REVERT: B 1085 ASP cc_start: 0.7214 (t0) cc_final: 0.6810 (t70) REVERT: B 1115 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 1118 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7000 (mp10) REVERT: C 157 ASN cc_start: 0.7607 (m110) cc_final: 0.7303 (m-40) REVERT: C 165 LEU cc_start: 0.8561 (mt) cc_final: 0.8321 (mt) REVERT: C 172 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5729 (pp) REVERT: C 222 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7023 (ttp-170) REVERT: C 232 LEU cc_start: 0.8621 (tp) cc_final: 0.8339 (tt) outliers start: 69 outliers final: 45 residues processed: 256 average time/residue: 0.0980 time to fit residues: 37.4594 Evaluate side-chains 222 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 1055 THR Chi-restraints excluded: chain B residue 1074 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118990 restraints weight = 16221.773| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.48 r_work: 0.3195 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12710 Z= 0.123 Angle : 0.593 8.680 17224 Z= 0.297 Chirality : 0.050 0.349 1865 Planarity : 0.003 0.037 2110 Dihedral : 12.397 150.164 1931 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.66 % Allowed : 16.49 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.22), residues: 1421 helix: -0.44 (0.22), residues: 595 sheet: -3.20 (0.34), residues: 174 loop : -2.43 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1112 TYR 0.012 0.001 TYR B1036 PHE 0.023 0.001 PHE B 225 TRP 0.007 0.001 TRP B 999 HIS 0.007 0.001 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12710) covalent geometry : angle 0.59278 / 0.30 (17224) hydrogen bonds : bond 0.03242 / 2.09 ( 447) hydrogen bonds : angle 4.74179 / 3.15 ( 1258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8086 (mm-30) REVERT: B 26 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7486 (tttm) REVERT: B 173 PHE cc_start: 0.7660 (t80) cc_final: 0.7361 (t80) REVERT: B 221 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5858 (tp30) REVERT: B 331 TYR cc_start: 0.8125 (m-80) cc_final: 0.7662 (m-80) REVERT: B 433 GLU cc_start: 0.9042 (tp30) cc_final: 0.8725 (tp30) REVERT: B 474 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: B 531 MET cc_start: 0.8844 (ttt) cc_final: 0.8532 (mtp) REVERT: B 752 LYS cc_start: 0.8703 (mptt) cc_final: 0.8289 (mmtm) REVERT: B 862 ASN cc_start: 0.8540 (t0) cc_final: 0.8305 (p0) REVERT: B 864 ASN cc_start: 0.9133 (t0) cc_final: 0.8885 (t0) REVERT: B 889 ASN cc_start: 0.7489 (m-40) cc_final: 0.6743 (t0) REVERT: B 893 ILE cc_start: 0.8857 (tt) cc_final: 0.8564 (tt) REVERT: B 945 LYS cc_start: 0.8080 (tptm) cc_final: 0.7744 (ttpt) REVERT: B 986 MET cc_start: 0.8848 (mtt) cc_final: 0.8587 (mtt) REVERT: B 1037 VAL cc_start: 0.8570 (m) cc_final: 0.8325 (m) REVERT: B 1056 ASP cc_start: 0.8345 (t0) cc_final: 0.7803 (t0) REVERT: B 1085 ASP cc_start: 0.7335 (t0) cc_final: 0.7005 (t70) REVERT: B 1115 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 1118 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7047 (mp10) REVERT: B 1189 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.6650 (mtt180) REVERT: C 137 ASP cc_start: 0.8542 (t70) cc_final: 0.8239 (t70) REVERT: C 157 ASN cc_start: 0.7742 (m110) cc_final: 0.7462 (m-40) REVERT: C 165 LEU cc_start: 0.8611 (mt) cc_final: 0.8411 (mt) REVERT: C 172 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5581 (pp) REVERT: C 222 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7126 (ttp-170) REVERT: C 232 LEU cc_start: 0.8660 (tp) cc_final: 0.8411 (tt) outliers start: 61 outliers final: 29 residues processed: 245 average time/residue: 0.1001 time to fit residues: 36.4848 Evaluate side-chains 209 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113462 restraints weight = 15603.368| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.57 r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12710 Z= 0.116 Angle : 0.580 8.186 17224 Z= 0.289 Chirality : 0.049 0.323 1865 Planarity : 0.003 0.035 2110 Dihedral : 12.126 151.368 1916 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.20 % Allowed : 16.95 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.22), residues: 1421 helix: -0.01 (0.22), residues: 595 sheet: -3.01 (0.35), residues: 167 loop : -2.21 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.012 0.001 TYR B 294 PHE 0.025 0.001 PHE B 225 TRP 0.017 0.001 TRP A 178 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12710) covalent geometry : angle 0.57980 / 0.29 (17224) hydrogen bonds : bond 0.03045 / 1.98 ( 447) hydrogen bonds : angle 4.50099 / 2.98 ( 1258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8355 (mm-30) REVERT: A 227 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8017 (mm-30) REVERT: B 26 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7554 (tttp) REVERT: B 173 PHE cc_start: 0.7779 (t80) cc_final: 0.7511 (t80) REVERT: B 221 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5664 (tp30) REVERT: B 319 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8351 (mmtt) REVERT: B 331 TYR cc_start: 0.8143 (m-80) cc_final: 0.7757 (m-80) REVERT: B 433 GLU cc_start: 0.8986 (tp30) cc_final: 0.8733 (tp30) REVERT: B 474 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 531 MET cc_start: 0.8787 (ttt) cc_final: 0.8541 (mtp) REVERT: B 752 LYS cc_start: 0.8785 (mptt) cc_final: 0.8434 (mmtm) REVERT: B 864 ASN cc_start: 0.9012 (t0) cc_final: 0.8701 (t0) REVERT: B 889 ASN cc_start: 0.7517 (m-40) cc_final: 0.6851 (t0) REVERT: B 893 ILE cc_start: 0.8982 (tt) cc_final: 0.8698 (tt) REVERT: B 986 MET cc_start: 0.8910 (mtt) cc_final: 0.8681 (mtt) REVERT: B 1033 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.6911 (ttm-80) REVERT: B 1037 VAL cc_start: 0.8714 (m) cc_final: 0.8456 (m) REVERT: B 1056 ASP cc_start: 0.8217 (t0) cc_final: 0.7685 (t0) REVERT: B 1085 ASP cc_start: 0.7385 (t0) cc_final: 0.7156 (t70) REVERT: B 1087 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7126 (tt0) REVERT: B 1115 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (mm) REVERT: B 1118 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7101 (mp10) REVERT: B 1189 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6802 (mtt180) REVERT: C 135 GLU cc_start: 0.8236 (tp30) cc_final: 0.7838 (tp30) REVERT: C 157 ASN cc_start: 0.7873 (m110) cc_final: 0.7606 (m-40) REVERT: C 165 LEU cc_start: 0.8633 (mt) cc_final: 0.8429 (mt) REVERT: C 172 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5704 (pp) REVERT: C 232 LEU cc_start: 0.8662 (tp) cc_final: 0.8432 (tt) outliers start: 55 outliers final: 35 residues processed: 232 average time/residue: 0.1009 time to fit residues: 34.7737 Evaluate side-chains 214 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117908 restraints weight = 16088.395| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.46 r_work: 0.3195 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12710 Z= 0.144 Angle : 0.592 8.286 17224 Z= 0.295 Chirality : 0.050 0.383 1865 Planarity : 0.003 0.038 2110 Dihedral : 11.980 147.375 1914 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.50 % Allowed : 17.25 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1421 helix: 0.12 (0.22), residues: 609 sheet: -2.89 (0.35), residues: 163 loop : -2.06 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.016 0.001 TYR B1124 PHE 0.028 0.001 PHE B 225 TRP 0.020 0.001 TRP A 178 HIS 0.002 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (12710) covalent geometry : angle 0.59151 / 0.30 (17224) hydrogen bonds : bond 0.03174 / 2.06 ( 447) hydrogen bonds : angle 4.45727 / 2.94 ( 1258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8154 (mm-30) REVERT: B 173 PHE cc_start: 0.7654 (t80) cc_final: 0.7409 (t80) REVERT: B 221 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5555 (tp30) REVERT: B 319 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8295 (mmtm) REVERT: B 331 TYR cc_start: 0.8022 (m-80) cc_final: 0.7623 (m-80) REVERT: B 433 GLU cc_start: 0.9109 (tp30) cc_final: 0.8818 (tp30) REVERT: B 474 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 531 MET cc_start: 0.8988 (ttt) cc_final: 0.8629 (mtp) REVERT: B 558 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.5785 (mmt) REVERT: B 752 LYS cc_start: 0.8683 (mptt) cc_final: 0.8328 (mmtm) REVERT: B 864 ASN cc_start: 0.9134 (t0) cc_final: 0.8832 (t0) REVERT: B 889 ASN cc_start: 0.7596 (m-40) cc_final: 0.6878 (t0) REVERT: B 893 ILE cc_start: 0.8879 (tt) cc_final: 0.8587 (tt) REVERT: B 986 MET cc_start: 0.8805 (mtt) cc_final: 0.8532 (mtt) REVERT: B 999 TRP cc_start: 0.8702 (m-10) cc_final: 0.8102 (m100) REVERT: B 1037 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8237 (m) REVERT: B 1056 ASP cc_start: 0.8382 (t0) cc_final: 0.7845 (t0) REVERT: B 1085 ASP cc_start: 0.7558 (t0) cc_final: 0.7150 (t70) REVERT: B 1087 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7131 (tt0) REVERT: B 1115 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 1118 GLN cc_start: 0.7551 (mm-40) cc_final: 0.6910 (mp10) REVERT: B 1189 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6746 (mtt180) REVERT: C 135 GLU cc_start: 0.8183 (tp30) cc_final: 0.7817 (tp30) REVERT: C 137 ASP cc_start: 0.8607 (t70) cc_final: 0.8283 (t70) REVERT: C 157 ASN cc_start: 0.7870 (m110) cc_final: 0.7614 (m-40) REVERT: C 172 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5635 (pp) REVERT: C 232 LEU cc_start: 0.8571 (tp) cc_final: 0.8342 (tt) outliers start: 59 outliers final: 44 residues processed: 222 average time/residue: 0.0975 time to fit residues: 32.4818 Evaluate side-chains 220 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1141 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118833 restraints weight = 15974.029| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.62 r_work: 0.3197 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12710 Z= 0.124 Angle : 0.574 8.370 17224 Z= 0.284 Chirality : 0.049 0.305 1865 Planarity : 0.003 0.036 2110 Dihedral : 11.959 146.745 1913 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.89 % Allowed : 18.17 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1421 helix: 0.31 (0.22), residues: 610 sheet: -2.77 (0.37), residues: 157 loop : -1.99 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.012 0.001 TYR B 294 PHE 0.028 0.001 PHE B 225 TRP 0.025 0.001 TRP A 178 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12710) covalent geometry : angle 0.57355 / 0.28 (17224) hydrogen bonds : bond 0.02978 / 1.94 ( 447) hydrogen bonds : angle 4.34377 / 2.87 ( 1258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 227 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8124 (mm-30) REVERT: B 173 PHE cc_start: 0.7587 (t80) cc_final: 0.7371 (t80) REVERT: B 221 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5560 (tp30) REVERT: B 319 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8297 (mmtt) REVERT: B 331 TYR cc_start: 0.8077 (m-80) cc_final: 0.7736 (m-80) REVERT: B 433 GLU cc_start: 0.9031 (tp30) cc_final: 0.8759 (tp30) REVERT: B 474 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: B 531 MET cc_start: 0.8804 (ttt) cc_final: 0.8461 (mtp) REVERT: B 558 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5694 (mmt) REVERT: B 752 LYS cc_start: 0.8666 (mptt) cc_final: 0.8318 (mmtm) REVERT: B 864 ASN cc_start: 0.9016 (t0) cc_final: 0.8754 (t0) REVERT: B 889 ASN cc_start: 0.7509 (m-40) cc_final: 0.6800 (t0) REVERT: B 893 ILE cc_start: 0.8860 (tt) cc_final: 0.8572 (tt) REVERT: B 999 TRP cc_start: 0.8604 (m-10) cc_final: 0.8063 (m100) REVERT: B 1037 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8350 (m) REVERT: B 1056 ASP cc_start: 0.8233 (t0) cc_final: 0.7680 (t0) REVERT: B 1085 ASP cc_start: 0.7502 (t0) cc_final: 0.7277 (t70) REVERT: B 1115 LEU cc_start: 0.8892 (mm) cc_final: 0.8550 (mm) REVERT: B 1118 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7048 (mp10) REVERT: B 1189 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.6705 (mtt180) REVERT: C 135 GLU cc_start: 0.8218 (tp30) cc_final: 0.7817 (tp30) REVERT: C 157 ASN cc_start: 0.7836 (m110) cc_final: 0.7593 (m-40) REVERT: C 172 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5688 (pp) REVERT: C 232 LEU cc_start: 0.8615 (tp) cc_final: 0.8392 (tt) outliers start: 51 outliers final: 38 residues processed: 217 average time/residue: 0.0942 time to fit residues: 30.5612 Evaluate side-chains 214 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1141 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 123 optimal weight: 0.0370 chunk 129 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114472 restraints weight = 15868.802| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.67 r_work: 0.3216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12710 Z= 0.112 Angle : 0.561 8.460 17224 Z= 0.278 Chirality : 0.048 0.299 1865 Planarity : 0.003 0.037 2110 Dihedral : 11.787 145.586 1911 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.89 % Allowed : 18.78 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.23), residues: 1421 helix: 0.48 (0.22), residues: 612 sheet: -2.74 (0.37), residues: 158 loop : -1.93 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.011 0.001 TYR B 294 PHE 0.028 0.001 PHE B 225 TRP 0.016 0.001 TRP A 178 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12710) covalent geometry : angle 0.56086 / 0.28 (17224) hydrogen bonds : bond 0.02858 / 1.87 ( 447) hydrogen bonds : angle 4.25236 / 2.81 ( 1258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 128 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 221 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5636 (tp30) REVERT: B 277 TYR cc_start: 0.8217 (m-10) cc_final: 0.8013 (m-10) REVERT: B 319 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8333 (mmtt) REVERT: B 331 TYR cc_start: 0.8060 (m-80) cc_final: 0.7775 (m-80) REVERT: B 433 GLU cc_start: 0.9011 (tp30) cc_final: 0.8788 (tp30) REVERT: B 474 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: B 531 MET cc_start: 0.8826 (ttt) cc_final: 0.8564 (mtp) REVERT: B 558 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.5736 (mmt) REVERT: B 752 LYS cc_start: 0.8730 (mptt) cc_final: 0.8388 (mmtm) REVERT: B 864 ASN cc_start: 0.8914 (t0) cc_final: 0.8678 (t0) REVERT: B 877 ASP cc_start: 0.8579 (t0) cc_final: 0.8325 (m-30) REVERT: B 889 ASN cc_start: 0.7582 (m-40) cc_final: 0.6818 (t0) REVERT: B 893 ILE cc_start: 0.8930 (tt) cc_final: 0.8642 (tt) REVERT: B 1033 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7432 (ttm-80) REVERT: B 1037 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8373 (m) REVERT: B 1056 ASP cc_start: 0.8219 (t0) cc_final: 0.7680 (t0) REVERT: B 1115 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8625 (mm) REVERT: B 1118 GLN cc_start: 0.7582 (mm-40) cc_final: 0.6984 (mp10) REVERT: B 1189 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6781 (mtt180) REVERT: C 135 GLU cc_start: 0.8239 (tp30) cc_final: 0.7856 (tp30) REVERT: C 157 ASN cc_start: 0.7860 (m110) cc_final: 0.7642 (m-40) REVERT: C 172 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5710 (pp) REVERT: C 222 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7123 (ttp-170) REVERT: C 232 LEU cc_start: 0.8702 (tp) cc_final: 0.8471 (tt) outliers start: 51 outliers final: 34 residues processed: 214 average time/residue: 0.1054 time to fit residues: 34.0986 Evaluate side-chains 208 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1141 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115535 restraints weight = 15604.160| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.83 r_work: 0.3157 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12710 Z= 0.157 Angle : 0.597 8.324 17224 Z= 0.295 Chirality : 0.051 0.387 1865 Planarity : 0.003 0.036 2110 Dihedral : 11.576 147.459 1901 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.43 % Allowed : 18.70 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 1421 helix: 0.45 (0.22), residues: 617 sheet: -2.68 (0.37), residues: 159 loop : -1.98 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.019 0.001 TYR B 562 PHE 0.029 0.001 PHE B 131 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12710) covalent geometry : angle 0.59695 / 0.29 (17224) hydrogen bonds : bond 0.03086 / 2.02 ( 447) hydrogen bonds : angle 4.33781 / 2.86 ( 1258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8099 (mt-10) REVERT: B 128 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 221 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5642 (tp30) REVERT: B 277 TYR cc_start: 0.8223 (m-10) cc_final: 0.7992 (m-80) REVERT: B 433 GLU cc_start: 0.9062 (tp30) cc_final: 0.8831 (tp30) REVERT: B 474 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: B 531 MET cc_start: 0.8867 (ttt) cc_final: 0.8603 (mtp) REVERT: B 558 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.5783 (mmt) REVERT: B 752 LYS cc_start: 0.8796 (mptt) cc_final: 0.8421 (mmtm) REVERT: B 864 ASN cc_start: 0.8973 (t0) cc_final: 0.8732 (t0) REVERT: B 889 ASN cc_start: 0.7626 (m-40) cc_final: 0.6909 (t0) REVERT: B 893 ILE cc_start: 0.8913 (tt) cc_final: 0.8615 (tt) REVERT: B 999 TRP cc_start: 0.8645 (m-10) cc_final: 0.8131 (m100) REVERT: B 1033 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7442 (ttm-80) REVERT: B 1037 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8450 (m) REVERT: B 1056 ASP cc_start: 0.8262 (t0) cc_final: 0.7722 (t0) REVERT: B 1086 TRP cc_start: 0.8715 (p-90) cc_final: 0.8330 (p-90) REVERT: B 1115 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8661 (mm) REVERT: B 1118 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7067 (mp10) REVERT: B 1189 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6774 (mtt180) REVERT: C 135 GLU cc_start: 0.8305 (tp30) cc_final: 0.7914 (tp30) REVERT: C 157 ASN cc_start: 0.7883 (m110) cc_final: 0.7656 (m-40) REVERT: C 172 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5714 (pp) REVERT: C 222 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7143 (ttp-170) REVERT: C 232 LEU cc_start: 0.8710 (tp) cc_final: 0.8474 (tt) outliers start: 58 outliers final: 41 residues processed: 218 average time/residue: 0.0974 time to fit residues: 32.3153 Evaluate side-chains 214 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1141 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B1178 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113919 restraints weight = 15586.891| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.55 r_work: 0.3209 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12710 Z= 0.123 Angle : 0.579 8.492 17224 Z= 0.287 Chirality : 0.049 0.299 1865 Planarity : 0.003 0.037 2110 Dihedral : 11.476 146.740 1898 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.97 % Allowed : 19.31 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.23), residues: 1421 helix: 0.64 (0.22), residues: 610 sheet: -2.52 (0.37), residues: 154 loop : -1.96 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.025 0.001 TYR B 562 PHE 0.029 0.001 PHE B 131 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12710) covalent geometry : angle 0.57936 / 0.29 (17224) hydrogen bonds : bond 0.02914 / 1.91 ( 447) hydrogen bonds : angle 4.26428 / 2.81 ( 1258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 227 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8186 (mm-30) REVERT: B 128 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 221 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5627 (tp30) REVERT: B 277 TYR cc_start: 0.8165 (m-10) cc_final: 0.7948 (m-80) REVERT: B 319 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8330 (mmtt) REVERT: B 331 TYR cc_start: 0.7924 (m-80) cc_final: 0.7700 (m-80) REVERT: B 433 GLU cc_start: 0.9172 (tp30) cc_final: 0.8925 (tp30) REVERT: B 474 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: B 531 MET cc_start: 0.8971 (ttt) cc_final: 0.8677 (mtp) REVERT: B 558 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.5742 (mmt) REVERT: B 752 LYS cc_start: 0.8748 (mptt) cc_final: 0.8373 (mmtm) REVERT: B 889 ASN cc_start: 0.7692 (m-40) cc_final: 0.6877 (t0) REVERT: B 893 ILE cc_start: 0.8938 (tt) cc_final: 0.8662 (tt) REVERT: B 999 TRP cc_start: 0.8751 (m-10) cc_final: 0.8165 (m100) REVERT: B 1033 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: B 1037 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (m) REVERT: B 1056 ASP cc_start: 0.8367 (t0) cc_final: 0.7771 (t0) REVERT: B 1086 TRP cc_start: 0.8738 (p-90) cc_final: 0.8352 (p-90) REVERT: B 1115 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 1118 GLN cc_start: 0.7570 (mm-40) cc_final: 0.6967 (mp10) REVERT: B 1189 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6817 (mtt180) REVERT: C 135 GLU cc_start: 0.8270 (tp30) cc_final: 0.7895 (tp30) REVERT: C 157 ASN cc_start: 0.7881 (m110) cc_final: 0.7649 (m-40) REVERT: C 172 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5676 (pp) REVERT: C 222 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7106 (ttp-170) REVERT: C 232 LEU cc_start: 0.8647 (tp) cc_final: 0.8416 (tt) outliers start: 52 outliers final: 40 residues processed: 206 average time/residue: 0.0930 time to fit residues: 28.7445 Evaluate side-chains 213 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 126 optimal weight: 0.0170 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121901 restraints weight = 15807.276| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.71 r_work: 0.3231 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12710 Z= 0.104 Angle : 0.564 8.510 17224 Z= 0.279 Chirality : 0.048 0.312 1865 Planarity : 0.003 0.037 2110 Dihedral : 11.372 145.063 1898 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.36 % Allowed : 19.62 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.23), residues: 1421 helix: 0.72 (0.22), residues: 617 sheet: -2.44 (0.37), residues: 152 loop : -1.94 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1054 TYR 0.024 0.001 TYR B 562 PHE 0.029 0.001 PHE B 131 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12710) covalent geometry : angle 0.56415 / 0.28 (17224) hydrogen bonds : bond 0.02733 / 1.79 ( 447) hydrogen bonds : angle 4.15551 / 2.74 ( 1258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.2884 (mtp) cc_final: 0.2547 (mtm) REVERT: A 184 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 227 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8081 (mm-30) REVERT: B 128 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7770 (mp) REVERT: B 221 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5554 (pp20) REVERT: B 232 GLU cc_start: 0.7519 (pt0) cc_final: 0.7220 (mp0) REVERT: B 277 TYR cc_start: 0.8188 (m-10) cc_final: 0.7905 (m-10) REVERT: B 319 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8282 (mmtt) REVERT: B 331 TYR cc_start: 0.7871 (m-80) cc_final: 0.7664 (m-80) REVERT: B 336 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8407 (pt) REVERT: B 433 GLU cc_start: 0.9080 (tp30) cc_final: 0.8842 (tp30) REVERT: B 531 MET cc_start: 0.8801 (ttt) cc_final: 0.8507 (mtp) REVERT: B 558 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5539 (mmt) REVERT: B 752 LYS cc_start: 0.8614 (mptt) cc_final: 0.8252 (mmtm) REVERT: B 877 ASP cc_start: 0.8483 (t0) cc_final: 0.8261 (m-30) REVERT: B 889 ASN cc_start: 0.7524 (m-40) cc_final: 0.6672 (t0) REVERT: B 893 ILE cc_start: 0.8792 (tt) cc_final: 0.8509 (tt) REVERT: B 935 ARG cc_start: 0.7464 (ptp90) cc_final: 0.7161 (ttp-110) REVERT: B 1033 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.7251 (ttm-80) REVERT: B 1037 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8288 (m) REVERT: B 1056 ASP cc_start: 0.8266 (t0) cc_final: 0.7702 (t0) REVERT: B 1086 TRP cc_start: 0.8624 (p-90) cc_final: 0.8258 (p-90) REVERT: B 1115 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 1118 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6875 (mp10) REVERT: B 1189 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6638 (mtt180) REVERT: C 135 GLU cc_start: 0.8158 (tp30) cc_final: 0.7766 (tp30) REVERT: C 157 ASN cc_start: 0.7832 (m110) cc_final: 0.7609 (m-40) REVERT: C 172 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5689 (pp) REVERT: C 174 GLU cc_start: 0.8055 (tp30) cc_final: 0.7853 (tm-30) REVERT: C 222 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7294 (ptm-80) REVERT: C 232 LEU cc_start: 0.8618 (tp) cc_final: 0.8400 (tt) outliers start: 44 outliers final: 32 residues processed: 208 average time/residue: 0.1028 time to fit residues: 31.6914 Evaluate side-chains 207 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 833 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124924 restraints weight = 15514.347| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.29 r_work: 0.3131 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12710 Z= 0.118 Angle : 0.577 8.600 17224 Z= 0.286 Chirality : 0.049 0.317 1865 Planarity : 0.003 0.036 2110 Dihedral : 11.264 146.287 1894 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.44 % Allowed : 19.54 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1421 helix: 0.76 (0.22), residues: 617 sheet: -2.39 (0.38), residues: 152 loop : -1.94 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1033 TYR 0.025 0.001 TYR B 562 PHE 0.031 0.001 PHE B 131 TRP 0.011 0.001 TRP A 178 HIS 0.002 0.000 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12710) covalent geometry : angle 0.57744 / 0.29 (17224) hydrogen bonds : bond 0.02812 / 1.84 ( 447) hydrogen bonds : angle 4.17365 / 2.75 ( 1258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.78 seconds wall clock time: 53 minutes 30.37 seconds (3210.37 seconds total)