Starting phenix.real_space_refine on Fri Sep 11 23:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rjg_4904/09_2026/6rjg_4904.cif" } resolution = 3.2 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 37 5.16 5 C 7318 2.51 5 N 2103 2.21 5 O 2639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 12220 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6633 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 794} Chain breaks: 5 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNAv2': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 2.46, per 1000 atoms: 0.20 Number of scatterers: 12220 At special positions: 0 Unit cell: (121.793, 140.462, 111.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 123 15.00 O 2639 8.00 N 2103 7.00 C 7318 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: 0.91 Conformation dependent library (CDL) restraints added in 435.3 milliseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 47.7% alpha, 14.4% beta 38 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.621A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 26 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 28 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.675A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.896A pdb=" N ASN A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.163A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.935A pdb=" N GLY A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 147 " --> pdb=" O GLY A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.559A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.617A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.833A pdb=" N TYR B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.554A pdb=" N ASN B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.688A pdb=" N LEU B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.128A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.716A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.759A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 73 removed outlier: 3.757A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.674A pdb=" N GLN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.748A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.346A pdb=" N ILE C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.922A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.949A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.755A pdb=" N THR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 382 removed outlier: 3.521A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.737A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.644A pdb=" N ASN C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.832A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.801A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 500 removed outlier: 3.568A pdb=" N ALA C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.687A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.594A pdb=" N PHE C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR A 128 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE C 827 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LYS C 848 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 7.535A pdb=" N MET B 121 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 131 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.919A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU C 809 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.586A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.805A pdb=" N ARG C 338 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 978 through 980 removed outlier: 7.039A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 978 through 980 removed outlier: 3.561A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.515A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2561 1.33 - 1.45: 3525 1.45 - 1.57: 6301 1.57 - 1.70: 241 1.70 - 1.82: 69 Bond restraints: 12697 Sorted by residual: bond pdb=" C1' DC E 28 " pdb=" N1 DC E 28 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.05e+01 bond pdb=" C3' DT E 16 " pdb=" O3' DT E 16 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" C1' DC E 35 " pdb=" N1 DC E 35 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DC E 28 " pdb=" O3' DC E 28 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.60e+00 ... (remaining 12692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 16955 2.45 - 4.91: 603 4.91 - 7.36: 57 7.36 - 9.81: 8 9.81 - 12.26: 3 Bond angle restraints: 17626 Sorted by residual: angle pdb=" O4' DT E 34 " pdb=" C4' DT E 34 " pdb=" C3' DT E 34 " ideal model delta sigma weight residual 106.00 102.42 3.58 6.00e-01 2.78e+00 3.57e+01 angle pdb=" O4' DT E 32 " pdb=" C4' DT E 32 " pdb=" C3' DT E 32 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.92e+01 angle pdb=" O4' DT E 29 " pdb=" C4' DT E 29 " pdb=" C3' DT E 29 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.71e+01 angle pdb=" O4' DC E 38 " pdb=" C4' DC E 38 " pdb=" C3' DC E 38 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DC E 38 " pdb=" C1' DC E 38 " pdb=" N1 DC E 38 " ideal model delta sigma weight residual 108.00 111.57 -3.57 7.00e-01 2.04e+00 2.60e+01 ... (remaining 17621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6166 17.72 - 35.44: 834 35.44 - 53.16: 318 53.16 - 70.88: 88 70.88 - 88.60: 20 Dihedral angle restraints: 7426 sinusoidal: 3979 harmonic: 3447 Sorted by residual: dihedral pdb=" C4' U D 8 " pdb=" C3' U D 8 " pdb=" C2' U D 8 " pdb=" C1' U D 8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.01 73.35 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" C4' U D 73 " pdb=" C3' U D 73 " pdb=" C2' U D 73 " pdb=" C1' U D 73 " ideal model delta sinusoidal sigma weight residual 36.35 -36.45 72.79 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' U D 74 " pdb=" C3' U D 74 " pdb=" C2' U D 74 " pdb=" C1' U D 74 " ideal model delta sinusoidal sigma weight residual 36.34 -36.40 72.74 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 7423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1607 0.082 - 0.165: 245 0.165 - 0.247: 84 0.247 - 0.330: 30 0.330 - 0.412: 3 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB ILE B 48 " pdb=" CA ILE B 48 " pdb=" CG1 ILE B 48 " pdb=" CG2 ILE B 48 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' U D 8 " pdb=" C3' U D 8 " pdb=" O2' U D 8 " pdb=" C1' U D 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.42 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 1966 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 260 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C THR C 260 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 260 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 261 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " 0.034 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 U D 7 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U D 7 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U D 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U D 7 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U D 7 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 7 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.025 2.00e-02 2.50e+03 1.83e-02 6.72e+00 pdb=" CG TYR B 26 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3439 2.82 - 3.34: 9580 3.34 - 3.86: 19773 3.86 - 4.38: 23494 4.38 - 4.90: 38482 Nonbonded interactions: 94768 Sorted by model distance: nonbonded pdb=" OD2 ASP C 878 " pdb=" OG1 THR C 881 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 68 " pdb=" NZ LYS A 99 " model vdw 2.339 3.120 nonbonded pdb=" OE1 GLU B 135 " pdb=" NE2 GLN B 151 " model vdw 2.341 3.120 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.362 3.040 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.377 3.040 ... (remaining 94763 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' selection = chain 'B' } 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: 1.570 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.710 Find NCS groups from input model: 0.070 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.008 0.071 12697 Z= 0.461 Angle : 1.038 12.264 17626 Z= 0.606 Chirality : 0.078 0.412 1969 Planarity : 0.006 0.063 1818 Dihedral : 18.526 88.602 5220 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.18), residues: 1164 helix: -2.16 (0.17), residues: 504 sheet: -1.79 (0.34), residues: 143 loop : -2.74 (0.21), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 921 TYR 0.043 0.003 TYR B 26 PHE 0.023 0.003 PHE C 818 TRP 0.010 0.002 TRP A 38 HIS 0.010 0.002 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.46 (12697) covalent geometry : angle 1.03764 / 0.61 (17626) hydrogen bonds : bond 0.15916 / 10.07 ( 506) hydrogen bonds : angle 6.55628 / 4.59 ( 1414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7669 (tmm) cc_final: 0.7324 (tmm) REVERT: B 155 LYS cc_start: 0.7389 (tptt) cc_final: 0.7167 (tptt) REVERT: B 156 ASP cc_start: 0.7731 (p0) cc_final: 0.7448 (t0) REVERT: C 273 TYR cc_start: 0.8173 (t80) cc_final: 0.7966 (t80) REVERT: C 447 MET cc_start: 0.6645 (ttt) cc_final: 0.6324 (ttp) REVERT: C 869 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8398 (tttt) REVERT: C 877 HIS cc_start: 0.6938 (m170) cc_final: 0.6612 (t-90) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.1180 time to fit residues: 32.8386 Evaluate side-chains 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 181 ASN B 88 ASN B 177 ASN B 178 ASN C 85 ASN C 142 ASN C 227 HIS C 276 GLN C 456 GLN C 505 ASN C 832 GLN C 855 GLN C 877 HIS ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123515 restraints weight = 16863.636| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.24 r_work: 0.3184 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12697 Z= 0.170 Angle : 0.957 18.236 17626 Z= 0.429 Chirality : 0.084 1.203 1969 Planarity : 0.004 0.039 1818 Dihedral : 17.468 122.199 2744 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.05 % Allowed : 12.14 % Favored : 86.81 % 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: -1.93 (0.21), residues: 1164 helix: -0.08 (0.21), residues: 509 sheet: -1.38 (0.38), residues: 122 loop : -2.50 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 120 TYR 0.022 0.001 TYR B 26 PHE 0.015 0.001 PHE A 67 TRP 0.012 0.001 TRP A 38 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12697) covalent geometry : angle 0.95734 / 0.43 (17626) hydrogen bonds : bond 0.05698 / 3.62 ( 506) hydrogen bonds : angle 4.91474 / 3.46 ( 1414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.475 Fit side-chains REVERT: B 15 MET cc_start: 0.8049 (tmm) cc_final: 0.7820 (tmm) REVERT: B 24 ASP cc_start: 0.7512 (m-30) cc_final: 0.7222 (m-30) REVERT: B 155 LYS cc_start: 0.7189 (tptt) cc_final: 0.6917 (tptt) REVERT: B 156 ASP cc_start: 0.7658 (p0) cc_final: 0.7142 (t0) REVERT: C 30 LYS cc_start: 0.7641 (tttt) cc_final: 0.7153 (tptt) REVERT: C 447 MET cc_start: 0.6544 (ttt) cc_final: 0.6239 (ttp) REVERT: C 877 HIS cc_start: 0.7680 (m-70) cc_final: 0.6958 (t-90) REVERT: C 1011 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7543 (mm-30) outliers start: 11 outliers final: 7 residues processed: 173 average time/residue: 0.1141 time to fit residues: 27.8854 Evaluate side-chains 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121632 restraints weight = 17206.736| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.23 r_work: 0.3152 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12697 Z= 0.194 Angle : 0.783 13.485 17626 Z= 0.373 Chirality : 0.064 0.938 1969 Planarity : 0.004 0.037 1818 Dihedral : 17.348 156.122 2741 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.58 % Allowed : 12.52 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1164 helix: 0.64 (0.22), residues: 512 sheet: -1.32 (0.37), residues: 140 loop : -2.35 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.019 0.002 TYR B 26 PHE 0.014 0.002 PHE A 67 TRP 0.014 0.001 TRP B 174 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (12697) covalent geometry : angle 0.78309 / 0.37 (17626) hydrogen bonds : bond 0.05708 / 3.59 ( 506) hydrogen bonds : angle 4.63285 / 3.26 ( 1414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.365 Fit side-chains REVERT: A 9 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 15 MET cc_start: 0.8082 (tmm) cc_final: 0.7865 (tmm) REVERT: B 155 LYS cc_start: 0.7246 (tptt) cc_final: 0.6970 (tptt) REVERT: B 156 ASP cc_start: 0.7705 (p0) cc_final: 0.7160 (t0) REVERT: C 30 LYS cc_start: 0.7670 (tttt) cc_final: 0.7183 (tptt) REVERT: C 447 MET cc_start: 0.6669 (ttt) cc_final: 0.6325 (ttp) REVERT: C 877 HIS cc_start: 0.7710 (m-70) cc_final: 0.6979 (t-90) REVERT: C 889 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7492 (tt) REVERT: C 923 TYR cc_start: 0.7253 (t80) cc_final: 0.6969 (t80) REVERT: C 1011 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7625 (mm-30) REVERT: C 1055 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8603 (m-10) outliers start: 27 outliers final: 17 residues processed: 170 average time/residue: 0.1012 time to fit residues: 24.9588 Evaluate side-chains 165 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 178 ASN B 181 ASN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121133 restraints weight = 17113.980| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.21 r_work: 0.3154 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12697 Z= 0.183 Angle : 0.728 13.675 17626 Z= 0.353 Chirality : 0.058 0.548 1969 Planarity : 0.004 0.037 1818 Dihedral : 17.264 157.722 2741 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.54 % Allowed : 12.52 % Favored : 83.94 % 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: -0.88 (0.23), residues: 1164 helix: 1.02 (0.22), residues: 511 sheet: -0.96 (0.40), residues: 141 loop : -2.22 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 111 TYR 0.016 0.002 TYR C 89 PHE 0.012 0.002 PHE C 882 TRP 0.019 0.001 TRP B 174 HIS 0.002 0.001 HIS C 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12697) covalent geometry : angle 0.72782 / 0.35 (17626) hydrogen bonds : bond 0.05442 / 3.44 ( 506) hydrogen bonds : angle 4.35692 / 3.08 ( 1414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 15 MET cc_start: 0.8071 (tmm) cc_final: 0.7813 (tmm) REVERT: B 155 LYS cc_start: 0.7367 (tptt) cc_final: 0.7088 (tptt) REVERT: C 30 LYS cc_start: 0.7652 (tttt) cc_final: 0.7179 (tptt) REVERT: C 447 MET cc_start: 0.6646 (ttt) cc_final: 0.6306 (ttp) REVERT: C 877 HIS cc_start: 0.7721 (m-70) cc_final: 0.6905 (t-90) REVERT: C 889 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (tt) REVERT: C 923 TYR cc_start: 0.7202 (t80) cc_final: 0.6955 (t80) REVERT: C 991 GLU cc_start: 0.8293 (tt0) cc_final: 0.7962 (tt0) REVERT: C 999 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (tp) REVERT: C 1011 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 1055 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8687 (m-10) outliers start: 37 outliers final: 28 residues processed: 184 average time/residue: 0.1047 time to fit residues: 27.6470 Evaluate side-chains 171 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 999 ILE Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 57 ASN C 348 HIS ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120256 restraints weight = 17085.056| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.18 r_work: 0.3142 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12697 Z= 0.210 Angle : 0.735 12.738 17626 Z= 0.357 Chirality : 0.057 0.431 1969 Planarity : 0.004 0.038 1818 Dihedral : 17.176 159.779 2741 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.11 % Allowed : 14.53 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1164 helix: 1.14 (0.22), residues: 513 sheet: -0.94 (0.40), residues: 141 loop : -2.17 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 385 TYR 0.018 0.002 TYR B 26 PHE 0.012 0.002 PHE C1044 TRP 0.026 0.002 TRP B 174 HIS 0.002 0.001 HIS C 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (12697) covalent geometry : angle 0.73482 / 0.36 (17626) hydrogen bonds : bond 0.05705 / 3.59 ( 506) hydrogen bonds : angle 4.34649 / 3.07 ( 1414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.9292 (tpt) cc_final: 0.8947 (tpt) REVERT: B 15 MET cc_start: 0.8095 (tmm) cc_final: 0.7813 (tmm) REVERT: B 111 ARG cc_start: 0.7691 (tpt-90) cc_final: 0.7340 (tpt-90) REVERT: B 139 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8060 (mm-30) REVERT: B 155 LYS cc_start: 0.7388 (tptt) cc_final: 0.7105 (tptt) REVERT: C 30 LYS cc_start: 0.7691 (tttt) cc_final: 0.7244 (tptt) REVERT: C 435 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 869 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8481 (ttmt) REVERT: C 877 HIS cc_start: 0.7708 (m-70) cc_final: 0.6817 (t-90) REVERT: C 889 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7503 (tt) REVERT: C 923 TYR cc_start: 0.7233 (t80) cc_final: 0.6991 (t80) REVERT: C 991 GLU cc_start: 0.8292 (tt0) cc_final: 0.7967 (tt0) REVERT: C 1011 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7716 (mm-30) REVERT: C 1055 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8709 (m-10) outliers start: 43 outliers final: 29 residues processed: 176 average time/residue: 0.1031 time to fit residues: 26.1229 Evaluate side-chains 171 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 80 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 137 GLN C 348 HIS ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123755 restraints weight = 17082.555| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.24 r_work: 0.3175 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12697 Z= 0.134 Angle : 0.666 11.606 17626 Z= 0.326 Chirality : 0.053 0.348 1969 Planarity : 0.003 0.037 1818 Dihedral : 17.068 158.918 2741 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.15 % Allowed : 15.30 % Favored : 81.55 % 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: -0.47 (0.24), residues: 1164 helix: 1.38 (0.22), residues: 515 sheet: -0.78 (0.41), residues: 144 loop : -2.04 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 385 TYR 0.016 0.001 TYR B 26 PHE 0.011 0.001 PHE C 882 TRP 0.025 0.001 TRP B 174 HIS 0.034 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12697) covalent geometry : angle 0.66603 / 0.33 (17626) hydrogen bonds : bond 0.04782 / 3.01 ( 506) hydrogen bonds : angle 4.21520 / 2.99 ( 1414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8201 (pt0) cc_final: 0.7639 (mt0) REVERT: A 149 MET cc_start: 0.9281 (tpt) cc_final: 0.8923 (tpt) REVERT: B 15 MET cc_start: 0.8054 (tmm) cc_final: 0.7793 (tmm) REVERT: B 111 ARG cc_start: 0.7580 (tpt-90) cc_final: 0.7378 (tpt-90) REVERT: B 155 LYS cc_start: 0.7337 (tptt) cc_final: 0.7024 (tptt) REVERT: B 156 ASP cc_start: 0.7637 (p0) cc_final: 0.7001 (t0) REVERT: C 30 LYS cc_start: 0.7654 (tttt) cc_final: 0.7183 (tptt) REVERT: C 435 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 869 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8458 (ttmt) REVERT: C 877 HIS cc_start: 0.7643 (m-70) cc_final: 0.6598 (t-90) REVERT: C 923 TYR cc_start: 0.7245 (t80) cc_final: 0.6981 (t80) REVERT: C 991 GLU cc_start: 0.8243 (tt0) cc_final: 0.8016 (tt0) REVERT: C 1011 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 1055 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8634 (m-10) outliers start: 33 outliers final: 23 residues processed: 169 average time/residue: 0.1097 time to fit residues: 26.5096 Evaluate side-chains 166 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123873 restraints weight = 17046.601| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.20 r_work: 0.3185 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12697 Z= 0.136 Angle : 0.648 11.748 17626 Z= 0.317 Chirality : 0.051 0.328 1969 Planarity : 0.003 0.036 1818 Dihedral : 16.925 159.193 2741 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.63 % Allowed : 15.01 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1164 helix: 1.53 (0.22), residues: 513 sheet: -0.69 (0.41), residues: 144 loop : -1.95 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 385 TYR 0.015 0.001 TYR B 26 PHE 0.011 0.001 PHE C 882 TRP 0.030 0.001 TRP B 174 HIS 0.002 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12697) covalent geometry : angle 0.64829 / 0.32 (17626) hydrogen bonds : bond 0.04618 / 2.92 ( 506) hydrogen bonds : angle 4.10385 / 2.92 ( 1414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.381 Fit side-chains REVERT: A 101 GLN cc_start: 0.8243 (pt0) cc_final: 0.7693 (mt0) REVERT: A 149 MET cc_start: 0.9283 (tpt) cc_final: 0.8928 (tpt) REVERT: B 15 MET cc_start: 0.8038 (tmm) cc_final: 0.7779 (tmm) REVERT: B 111 ARG cc_start: 0.7513 (tpt-90) cc_final: 0.7304 (tpt-90) REVERT: B 115 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6961 (pt) REVERT: B 139 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8025 (mm-30) REVERT: B 155 LYS cc_start: 0.7467 (tptt) cc_final: 0.7128 (tptt) REVERT: B 156 ASP cc_start: 0.7665 (p0) cc_final: 0.7084 (t0) REVERT: C 30 LYS cc_start: 0.7604 (tttt) cc_final: 0.7159 (tptt) REVERT: C 39 GLN cc_start: 0.8552 (pm20) cc_final: 0.8146 (pm20) REVERT: C 435 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8059 (mp) REVERT: C 450 LEU cc_start: 0.7204 (mt) cc_final: 0.6928 (mt) REVERT: C 862 MET cc_start: 0.8347 (tpp) cc_final: 0.7844 (tpp) REVERT: C 869 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8438 (ttmt) REVERT: C 877 HIS cc_start: 0.7581 (m-70) cc_final: 0.6648 (t-90) REVERT: C 923 TYR cc_start: 0.7291 (t80) cc_final: 0.7012 (t80) REVERT: C 981 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8777 (mp) REVERT: C 991 GLU cc_start: 0.8257 (tt0) cc_final: 0.8011 (tt0) REVERT: C 1011 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 1055 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8799 (m-80) outliers start: 38 outliers final: 25 residues processed: 177 average time/residue: 0.1043 time to fit residues: 26.3096 Evaluate side-chains 173 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN C 403 GLN ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120833 restraints weight = 17046.108| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.20 r_work: 0.3151 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12697 Z= 0.194 Angle : 0.699 13.365 17626 Z= 0.340 Chirality : 0.053 0.354 1969 Planarity : 0.003 0.036 1818 Dihedral : 16.925 160.964 2741 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.02 % Allowed : 15.01 % Favored : 80.98 % 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: -0.38 (0.24), residues: 1164 helix: 1.45 (0.22), residues: 513 sheet: -0.75 (0.41), residues: 141 loop : -1.97 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 385 TYR 0.016 0.002 TYR B 80 PHE 0.011 0.002 PHE C 412 TRP 0.030 0.002 TRP B 174 HIS 0.002 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (12697) covalent geometry : angle 0.69899 / 0.34 (17626) hydrogen bonds : bond 0.05333 / 3.37 ( 506) hydrogen bonds : angle 4.14375 / 2.93 ( 1414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.416 Fit side-chains REVERT: A 101 GLN cc_start: 0.8270 (pt0) cc_final: 0.7668 (mt0) REVERT: A 149 MET cc_start: 0.9299 (tpt) cc_final: 0.8952 (tpt) REVERT: B 15 MET cc_start: 0.8095 (tmm) cc_final: 0.7816 (tmm) REVERT: B 111 ARG cc_start: 0.7612 (tpt-90) cc_final: 0.7356 (tpt-90) REVERT: B 155 LYS cc_start: 0.7519 (tptt) cc_final: 0.7212 (tptt) REVERT: C 30 LYS cc_start: 0.7654 (tttt) cc_final: 0.7201 (tptt) REVERT: C 39 GLN cc_start: 0.8542 (pm20) cc_final: 0.8303 (pm20) REVERT: C 435 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 869 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8463 (ttmt) REVERT: C 877 HIS cc_start: 0.7647 (m-70) cc_final: 0.6549 (t-90) REVERT: C 923 TYR cc_start: 0.7288 (t80) cc_final: 0.6998 (t80) REVERT: C 991 GLU cc_start: 0.8281 (tt0) cc_final: 0.8017 (tt0) REVERT: C 1011 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 1055 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8888 (m-80) outliers start: 42 outliers final: 34 residues processed: 176 average time/residue: 0.1042 time to fit residues: 26.4093 Evaluate side-chains 179 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122894 restraints weight = 17035.250| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.27 r_work: 0.3163 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12697 Z= 0.154 Angle : 0.666 13.028 17626 Z= 0.325 Chirality : 0.052 0.333 1969 Planarity : 0.003 0.037 1818 Dihedral : 16.888 160.580 2741 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.02 % Allowed : 15.58 % Favored : 80.40 % 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: -0.27 (0.24), residues: 1164 helix: 1.53 (0.22), residues: 514 sheet: -0.72 (0.41), residues: 144 loop : -1.90 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.014 0.001 TYR B 26 PHE 0.012 0.001 PHE C 261 TRP 0.034 0.002 TRP B 174 HIS 0.001 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12697) covalent geometry : angle 0.66636 / 0.33 (17626) hydrogen bonds : bond 0.04863 / 3.06 ( 506) hydrogen bonds : angle 4.09256 / 2.90 ( 1414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.397 Fit side-chains REVERT: A 101 GLN cc_start: 0.8251 (pt0) cc_final: 0.7662 (mt0) REVERT: A 149 MET cc_start: 0.9298 (tpt) cc_final: 0.8939 (tpt) REVERT: B 15 MET cc_start: 0.8053 (tmm) cc_final: 0.7776 (tmm) REVERT: B 111 ARG cc_start: 0.7568 (tpt-90) cc_final: 0.7321 (tpt-90) REVERT: B 155 LYS cc_start: 0.7518 (tptt) cc_final: 0.7170 (tptt) REVERT: B 156 ASP cc_start: 0.7729 (p0) cc_final: 0.7185 (t0) REVERT: C 30 LYS cc_start: 0.7640 (tttt) cc_final: 0.7179 (tptt) REVERT: C 39 GLN cc_start: 0.8571 (pm20) cc_final: 0.7644 (pm20) REVERT: C 157 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 435 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 862 MET cc_start: 0.8313 (tpp) cc_final: 0.7832 (mpp) REVERT: C 869 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8448 (ttmt) REVERT: C 877 HIS cc_start: 0.7651 (m-70) cc_final: 0.6579 (t-90) REVERT: C 923 TYR cc_start: 0.7300 (t80) cc_final: 0.6993 (t80) REVERT: C 991 GLU cc_start: 0.8269 (tt0) cc_final: 0.7996 (tt0) REVERT: C 1011 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 1055 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8764 (m-80) outliers start: 42 outliers final: 33 residues processed: 173 average time/residue: 0.1033 time to fit residues: 25.9197 Evaluate side-chains 181 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN C 403 GLN ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122615 restraints weight = 17075.429| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.25 r_work: 0.3158 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12697 Z= 0.165 Angle : 0.673 13.562 17626 Z= 0.329 Chirality : 0.052 0.334 1969 Planarity : 0.003 0.034 1818 Dihedral : 16.867 160.746 2741 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.82 % Allowed : 15.58 % Favored : 80.59 % 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: -0.27 (0.24), residues: 1164 helix: 1.54 (0.22), residues: 514 sheet: -0.76 (0.41), residues: 144 loop : -1.91 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.015 0.001 TYR B 26 PHE 0.012 0.001 PHE C 412 TRP 0.033 0.002 TRP B 174 HIS 0.002 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (12697) covalent geometry : angle 0.67336 / 0.33 (17626) hydrogen bonds : bond 0.04968 / 3.14 ( 506) hydrogen bonds : angle 4.08514 / 2.89 ( 1414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.446 Fit side-chains REVERT: A 101 GLN cc_start: 0.8261 (pt0) cc_final: 0.7667 (mt0) REVERT: A 149 MET cc_start: 0.9296 (tpt) cc_final: 0.8948 (tpt) REVERT: A 156 ASP cc_start: 0.8369 (p0) cc_final: 0.8160 (p0) REVERT: B 15 MET cc_start: 0.8060 (tmm) cc_final: 0.7781 (tmm) REVERT: B 111 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.7237 (tpt-90) REVERT: B 155 LYS cc_start: 0.7540 (tptt) cc_final: 0.7194 (tptt) REVERT: B 156 ASP cc_start: 0.7804 (p0) cc_final: 0.7274 (t0) REVERT: C 30 LYS cc_start: 0.7640 (tttt) cc_final: 0.7182 (tptt) REVERT: C 39 GLN cc_start: 0.8596 (pm20) cc_final: 0.7707 (pm20) REVERT: C 157 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7375 (mt-10) REVERT: C 435 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8088 (mp) REVERT: C 869 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8455 (ttmt) REVERT: C 877 HIS cc_start: 0.7648 (m-70) cc_final: 0.6585 (t-90) REVERT: C 923 TYR cc_start: 0.7304 (t80) cc_final: 0.6987 (t80) REVERT: C 991 GLU cc_start: 0.8274 (tt0) cc_final: 0.8007 (tt0) REVERT: C 1011 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7740 (mm-30) REVERT: C 1055 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8865 (m-80) outliers start: 40 outliers final: 35 residues processed: 171 average time/residue: 0.1027 time to fit residues: 25.5733 Evaluate side-chains 181 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 HIS ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124186 restraints weight = 17009.507| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.17 r_work: 0.3189 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12697 Z= 0.128 Angle : 0.646 12.771 17626 Z= 0.317 Chirality : 0.050 0.319 1969 Planarity : 0.003 0.036 1818 Dihedral : 16.831 160.639 2741 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.15 % Allowed : 16.16 % Favored : 80.69 % 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: -0.16 (0.24), residues: 1164 helix: 1.67 (0.22), residues: 513 sheet: -0.67 (0.42), residues: 144 loop : -1.88 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.014 0.001 TYR B 26 PHE 0.011 0.001 PHE C 412 TRP 0.032 0.001 TRP B 174 HIS 0.001 0.000 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12697) covalent geometry : angle 0.64628 / 0.32 (17626) hydrogen bonds : bond 0.04542 / 2.87 ( 506) hydrogen bonds : angle 4.03033 / 2.85 ( 1414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.90 seconds wall clock time: 44 minutes 54.21 seconds (2694.21 seconds total)