Starting phenix.real_space_refine on Fri Jul 3 16:46:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r7c_24297/07_2026/7r7c_24297.cif" } resolution = 3.71 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= 0.001 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 225 5.49 5 S 42 5.16 5 C 8588 2.51 5 N 2672 2.21 5 O 3423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14950 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 4818 Inner-chain residues flagged as termini: ['pdbres=" A 12404 "'] Classifications: {'RNA': 226} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 9, 'rna3p_pur': 103, 'rna3p_pyr': 98} Link IDs: {'rna2p': 25, 'rna3p': 200} Chain breaks: 8 Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain: "r" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "w" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 106 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "7" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 841 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 759 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 3 Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 802 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "b" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Chain: "a" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1696 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 204} Time building chain proxies: 2.31, per 1000 atoms: 0.15 Number of scatterers: 14950 At special positions: 0 Unit cell: (105.84, 155.52, 138.24, 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 42 16.00 P 225 15.00 O 3423 8.00 N 2672 7.00 C 8588 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: 0.96 Conformation dependent library (CDL) restraints added in 509.7 milliseconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 43.0% alpha, 13.2% beta 61 base pairs and 113 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'l' and resid 5 through 18 Processing helix chain 'l' and resid 49 through 55 removed outlier: 3.576A pdb=" N LEU l 54 " --> pdb=" O HIS l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 58 No H-bonds generated for 'chain 'l' and resid 56 through 58' Processing helix chain 'l' and resid 59 through 63 removed outlier: 3.598A pdb=" N LEU l 63 " --> pdb=" O ARG l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 90 Processing helix chain 'l' and resid 100 through 102 No H-bonds generated for 'chain 'l' and resid 100 through 102' Processing helix chain 'l' and resid 103 through 109 removed outlier: 3.869A pdb=" N PHE l 107 " --> pdb=" O GLY l 103 " (cutoff:3.500A) Processing helix chain 'l' and resid 171 through 176 removed outlier: 4.251A pdb=" N ASP l 175 " --> pdb=" O GLU l 171 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU l 176 " --> pdb=" O TYR l 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 171 through 176' Processing helix chain 'm' and resid 161 through 165 Processing helix chain 'm' and resid 187 through 197 removed outlier: 3.612A pdb=" N GLN m 191 " --> pdb=" O SER m 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU m 192 " --> pdb=" O ALA m 188 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 213 removed outlier: 3.803A pdb=" N THR q 202 " --> pdb=" O THR q 198 " (cutoff:3.500A) Processing helix chain 'q' and resid 224 through 239 removed outlier: 3.567A pdb=" N VAL q 228 " --> pdb=" O ARG q 224 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP q 229 " --> pdb=" O GLY q 225 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU q 237 " --> pdb=" O LYS q 233 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 252 removed outlier: 4.089A pdb=" N LEU q 252 " --> pdb=" O LYS q 248 " (cutoff:3.500A) Processing helix chain 'q' and resid 254 through 264 Processing helix chain 'q' and resid 281 through 293 Processing helix chain 'q' and resid 319 through 324 Processing helix chain 'q' and resid 334 through 342 removed outlier: 4.464A pdb=" N VAL q 338 " --> pdb=" O SER q 334 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE q 339 " --> pdb=" O PHE q 335 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU q 341 " --> pdb=" O PRO q 337 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP q 342 " --> pdb=" O VAL q 338 " (cutoff:3.500A) Processing helix chain 'q' and resid 357 through 368 Processing helix chain 'q' and resid 379 through 393 removed outlier: 3.757A pdb=" N THR q 383 " --> pdb=" O ASN q 379 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS q 384 " --> pdb=" O LYS q 380 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER q 385 " --> pdb=" O SER q 381 " (cutoff:3.500A) Processing helix chain 'q' and resid 404 through 406 No H-bonds generated for 'chain 'q' and resid 404 through 406' Processing helix chain 'q' and resid 407 through 412 removed outlier: 3.879A pdb=" N VAL q 411 " --> pdb=" O GLU q 407 " (cutoff:3.500A) Processing helix chain 'q' and resid 435 through 440 Processing helix chain 'q' and resid 443 through 446 Processing helix chain 'q' and resid 447 through 462 removed outlier: 3.529A pdb=" N LEU q 451 " --> pdb=" O GLN q 447 " (cutoff:3.500A) Processing helix chain 'q' and resid 481 through 495 removed outlier: 4.498A pdb=" N ALA q 487 " --> pdb=" O GLU q 483 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL q 488 " --> pdb=" O GLU q 484 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE q 489 " --> pdb=" O ASP q 485 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU q 493 " --> pdb=" O ILE q 489 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS q 495 " --> pdb=" O TYR q 491 " (cutoff:3.500A) Processing helix chain 'q' and resid 522 through 528 removed outlier: 3.790A pdb=" N LYS q 526 " --> pdb=" O PRO q 523 " (cutoff:3.500A) Processing helix chain 'r' and resid 165 through 169 removed outlier: 3.709A pdb=" N GLU r 169 " --> pdb=" O VAL r 166 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'w' and resid 828 through 836 Processing helix chain '7' and resid 25 through 30 Processing helix chain '7' and resid 46 through 58 Processing helix chain '7' and resid 104 through 116 removed outlier: 4.155A pdb=" N LEU 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 147 removed outlier: 3.694A pdb=" N LYS 7 147 " --> pdb=" O GLU 7 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'J' and resid 246 through 265 Processing helix chain 'J' and resid 281 through 314 removed outlier: 3.726A pdb=" N GLN J 310 " --> pdb=" O ARG J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 339 removed outlier: 3.521A pdb=" N VAL J 318 " --> pdb=" O PHE J 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'b' and resid 104 through 117 removed outlier: 4.041A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU b 115 " --> pdb=" O ASP b 111 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS b 117 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 142 Processing helix chain 'a' and resid 5 through 22 removed outlier: 3.680A pdb=" N GLU a 22 " --> pdb=" O LYS a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 79 removed outlier: 3.736A pdb=" N SER a 79 " --> pdb=" O ASP a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 93 removed outlier: 4.187A pdb=" N LEU a 93 " --> pdb=" O ASP a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 108 removed outlier: 3.651A pdb=" N TYR a 107 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN a 108 " --> pdb=" O SER a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 118 removed outlier: 4.281A pdb=" N LYS a 118 " --> pdb=" O GLU a 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 114 through 118' Processing helix chain 'a' and resid 119 through 124 Processing helix chain 'a' and resid 126 through 131 Processing helix chain 'a' and resid 143 through 153 removed outlier: 3.605A pdb=" N ASP a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 194 removed outlier: 3.550A pdb=" N LEU a 179 " --> pdb=" O GLU a 175 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU a 193 " --> pdb=" O PHE a 189 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU a 194 " --> pdb=" O PHE a 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'l' and resid 2 through 3 removed outlier: 6.796A pdb=" N VAL l 44 " --> pdb=" O LEU l 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE l 68 " --> pdb=" O TYR l 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'l' and resid 65 through 66 removed outlier: 6.408A pdb=" N LEU q 350 " --> pdb=" O LEU q 419 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE q 418 " --> pdb=" O VAL q 474 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'l' and resid 96 through 99 removed outlier: 6.329A pdb=" N ILE l 97 " --> pdb=" O PHE l 134 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA l 135 " --> pdb=" O PRO l 140 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU l 141 " --> pdb=" O ASP l 168 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP l 168 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE l 143 " --> pdb=" O GLN l 166 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL l 113 " --> pdb=" O VAL l 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'm' and resid 170 through 173 removed outlier: 3.982A pdb=" N GLY m 172 " --> pdb=" O ILE m 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'q' and resid 294 through 298 removed outlier: 7.261A pdb=" N ASN q 295 " --> pdb=" O PHE q 310 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE q 271 " --> pdb=" O ILE q 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'r' and resid 181 through 186 removed outlier: 3.687A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL r 200 " --> pdb=" O GLU r 222 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU r 222 " --> pdb=" O VAL r 200 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA r 257 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN r 183 " --> pdb=" O ALA r 257 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU r 259 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR r 185 " --> pdb=" O LEU r 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 88 through 90 Processing sheet with id=AA8, first strand: chain '7' and resid 88 through 90 Processing sheet with id=AA9, first strand: chain 'a' and resid 164 through 171 removed outlier: 6.933A pdb=" N CYS a 164 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU a 38 " --> pdb=" O CYS a 164 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA a 166 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL a 36 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA a 168 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU a 34 " --> pdb=" O ALA a 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 50 through 54 Processing sheet with id=AB2, first strand: chain 'a' and resid 66 through 68 removed outlier: 3.641A pdb=" N THR a 136 " --> pdb=" O PHE a 110 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 113 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3356 1.33 - 1.45: 4232 1.45 - 1.57: 7579 1.57 - 1.69: 441 1.69 - 1.81: 69 Bond restraints: 15677 Sorted by residual: bond pdb=" O5' C 12960 " pdb=" C5' C 12960 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" O5' G 12972 " pdb=" C5' G 12972 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.74e+00 bond pdb=" O5' U 1 960 " pdb=" C5' U 1 960 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.56e+00 bond pdb=" C1' G 12972 " pdb=" N9 G 12972 " ideal model delta sigma weight residual 1.475 1.459 0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" CA ILE m 180 " pdb=" CB ILE m 180 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.03e+00 ... (remaining 15672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 21707 1.52 - 3.03: 395 3.03 - 4.55: 68 4.55 - 6.07: 20 6.07 - 7.58: 4 Bond angle restraints: 22194 Sorted by residual: angle pdb=" N GLU 7 53 " pdb=" CA GLU 7 53 " pdb=" CB GLU 7 53 " ideal model delta sigma weight residual 110.12 115.23 -5.11 1.47e+00 4.63e-01 1.21e+01 angle pdb=" C3' C 1 870 " pdb=" O3' C 1 870 " pdb=" P G 1 871 " ideal model delta sigma weight residual 120.20 124.85 -4.65 1.50e+00 4.44e-01 9.60e+00 angle pdb=" C VAL q 538 " pdb=" N ASP q 539 " pdb=" CA ASP q 539 " ideal model delta sigma weight residual 122.19 129.31 -7.12 2.30e+00 1.89e-01 9.59e+00 angle pdb=" O3' C 1 870 " pdb=" C3' C 1 870 " pdb=" C2' C 1 870 " ideal model delta sigma weight residual 113.70 118.19 -4.49 1.50e+00 4.44e-01 8.94e+00 angle pdb=" O3' A 12419 " pdb=" C3' A 12419 " pdb=" C2' A 12419 " ideal model delta sigma weight residual 113.70 118.03 -4.33 1.50e+00 4.44e-01 8.33e+00 ... (remaining 22189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 8774 35.39 - 70.78: 247 70.78 - 106.17: 29 106.17 - 141.57: 4 141.57 - 176.96: 4 Dihedral angle restraints: 9058 sinusoidal: 5373 harmonic: 3685 Sorted by residual: dihedral pdb=" O4' C 1 959 " pdb=" C1' C 1 959 " pdb=" N1 C 1 959 " pdb=" C2 C 1 959 " ideal model delta sinusoidal sigma weight residual 200.00 39.76 160.24 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U 12829 " pdb=" C1' U 12829 " pdb=" N1 U 12829 " pdb=" C2 U 12829 " ideal model delta sinusoidal sigma weight residual 200.00 53.83 146.17 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 200.00 75.85 124.15 1 1.50e+01 4.44e-03 6.66e+01 ... (remaining 9055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2339 0.052 - 0.104: 299 0.104 - 0.156: 48 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA GLN b 127 " pdb=" N GLN b 127 " pdb=" C GLN b 127 " pdb=" CB GLN b 127 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' A 12419 " pdb=" C4' A 12419 " pdb=" O3' A 12419 " pdb=" C2' A 12419 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C3' U 1 960 " pdb=" C4' U 1 960 " pdb=" O3' U 1 960 " pdb=" C2' U 1 960 " both_signs ideal model delta sigma weight residual False -2.48 -2.63 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2685 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12975 " -0.022 2.00e-02 2.50e+03 1.09e-02 2.68e+00 pdb=" N1 U 12975 " 0.022 2.00e-02 2.50e+03 pdb=" C2 U 12975 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 12975 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U 12975 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U 12975 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U 12975 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U 12975 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U 12975 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12451 " -0.022 2.00e-02 2.50e+03 9.30e-03 2.59e+00 pdb=" N9 G 12451 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G 12451 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 12451 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 12451 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 12451 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G 12451 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G 12451 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 12451 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G 12451 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 12451 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 12451 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12974 " -0.020 2.00e-02 2.50e+03 1.04e-02 2.46e+00 pdb=" N1 U 12974 " 0.022 2.00e-02 2.50e+03 pdb=" C2 U 12974 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U 12974 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U 12974 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U 12974 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U 12974 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U 12974 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U 12974 " 0.002 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 627 2.69 - 3.24: 14190 3.24 - 3.79: 25491 3.79 - 4.35: 32741 4.35 - 4.90: 49193 Nonbonded interactions: 122242 Sorted by model distance: nonbonded pdb=" O2' C 1 870 " pdb=" OP1 G 1 871 " model vdw 2.134 3.040 nonbonded pdb=" N2 G 12451 " pdb=" O2 C 12496 " model vdw 2.219 2.496 nonbonded pdb=" OG1 THR A 119 " pdb=" OD1 ASP A 121 " model vdw 2.223 3.040 nonbonded pdb=" O CYS l 69 " pdb=" OG1 THR l 84 " model vdw 2.228 3.040 nonbonded pdb=" O ASP a 150 " pdb=" OG1 THR a 154 " model vdw 2.237 3.040 ... (remaining 122237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.040 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.002 0.034 15677 Z= 0.111 Angle : 0.530 7.585 22194 Z= 0.276 Chirality : 0.035 0.260 2688 Planarity : 0.003 0.040 1989 Dihedral : 15.841 176.958 6666 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1239 helix: 0.85 (0.24), residues: 479 sheet: -0.95 (0.44), residues: 148 loop : -0.81 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 130 TYR 0.013 0.001 TYR q 516 PHE 0.023 0.001 PHE q 253 TRP 0.004 0.001 TRP r 239 HIS 0.002 0.000 HIS q 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (15677) covalent geometry : angle 0.53047 / 0.28 (22194) hydrogen bonds : bond 0.15800 / 9.28 ( 538) hydrogen bonds : angle 5.83847 / 3.37 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 541 PHE cc_start: 0.7360 (t80) cc_final: 0.6990 (t80) REVERT: r 244 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7553 (tm-30) REVERT: r 246 THR cc_start: 0.8621 (p) cc_final: 0.8252 (p) REVERT: A 47 HIS cc_start: 0.6079 (t70) cc_final: 0.5806 (t-90) REVERT: J 304 GLU cc_start: 0.7966 (tp30) cc_final: 0.7333 (tp30) REVERT: a 181 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7135 (tm-30) REVERT: a 185 MET cc_start: 0.7542 (ptt) cc_final: 0.7161 (ptt) REVERT: a 215 ARG cc_start: 0.8426 (tpp-160) cc_final: 0.8150 (mmm160) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1326 time to fit residues: 38.9809 Evaluate side-chains 156 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... m 191 GLN r 179 GLN w 837 HIS 7 29 GLN A 195 HIS ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.094448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076034 restraints weight = 52019.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077352 restraints weight = 28234.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077581 restraints weight = 18468.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077802 restraints weight = 16329.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077813 restraints weight = 14748.695| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15677 Z= 0.118 Angle : 0.565 8.534 22194 Z= 0.285 Chirality : 0.036 0.216 2688 Planarity : 0.004 0.038 1989 Dihedral : 14.815 176.874 4061 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.81 % Allowed : 8.62 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1239 helix: 1.14 (0.24), residues: 485 sheet: -1.14 (0.43), residues: 154 loop : -0.65 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG r 170 TYR 0.019 0.001 TYR A 191 PHE 0.015 0.002 PHE r 194 TRP 0.003 0.001 TRP a 198 HIS 0.003 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15677) covalent geometry : angle 0.56540 / 0.28 (22194) hydrogen bonds : bond 0.05143 / 3.09 ( 538) hydrogen bonds : angle 4.52937 / 2.61 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 367 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: r 195 LEU cc_start: 0.8834 (mp) cc_final: 0.8484 (mt) REVERT: r 244 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7813 (tm-30) REVERT: r 246 THR cc_start: 0.8639 (p) cc_final: 0.8310 (p) REVERT: A 47 HIS cc_start: 0.6461 (t70) cc_final: 0.6237 (t-90) REVERT: A 51 ASP cc_start: 0.7558 (m-30) cc_final: 0.7292 (m-30) REVERT: J 261 LEU cc_start: 0.3943 (mm) cc_final: 0.3671 (mm) REVERT: J 283 GLU cc_start: 0.7192 (tp30) cc_final: 0.6938 (tp30) REVERT: J 286 ASP cc_start: 0.7768 (m-30) cc_final: 0.7298 (t0) REVERT: J 304 GLU cc_start: 0.8016 (tp30) cc_final: 0.7355 (tp30) REVERT: a 181 GLN cc_start: 0.8649 (tm-30) cc_final: 0.7568 (tm-30) outliers start: 9 outliers final: 3 residues processed: 183 average time/residue: 0.1294 time to fit residues: 34.1460 Evaluate side-chains 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 367 MET Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... r 179 GLN ** a 119 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.093288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074158 restraints weight = 52431.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075992 restraints weight = 28940.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076585 restraints weight = 16298.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076638 restraints weight = 13526.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076673 restraints weight = 12959.116| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15677 Z= 0.132 Angle : 0.548 8.766 22194 Z= 0.278 Chirality : 0.036 0.223 2688 Planarity : 0.004 0.032 1989 Dihedral : 14.841 176.572 4061 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.99 % Allowed : 12.21 % Favored : 86.80 % 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: 0.01 (0.25), residues: 1239 helix: 1.26 (0.24), residues: 485 sheet: -1.15 (0.43), residues: 159 loop : -0.66 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 137 TYR 0.019 0.002 TYR A 191 PHE 0.014 0.002 PHE a 190 TRP 0.004 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15677) covalent geometry : angle 0.54801 / 0.28 (22194) hydrogen bonds : bond 0.04742 / 2.85 ( 538) hydrogen bonds : angle 4.33278 / 2.46 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 541 PHE cc_start: 0.7770 (t80) cc_final: 0.7539 (t80) REVERT: r 244 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7809 (tm-30) REVERT: r 246 THR cc_start: 0.8652 (p) cc_final: 0.8297 (p) REVERT: r 250 ASP cc_start: 0.7339 (t0) cc_final: 0.7097 (t0) REVERT: A 47 HIS cc_start: 0.6573 (t70) cc_final: 0.6139 (t-90) REVERT: A 51 ASP cc_start: 0.7693 (m-30) cc_final: 0.7439 (m-30) REVERT: A 214 GLU cc_start: 0.6296 (pp20) cc_final: 0.6065 (pp20) REVERT: J 251 LEU cc_start: 0.3659 (OUTLIER) cc_final: 0.3443 (mm) REVERT: J 261 LEU cc_start: 0.4097 (mm) cc_final: 0.3890 (mm) REVERT: J 283 GLU cc_start: 0.7186 (tp30) cc_final: 0.6903 (tp30) REVERT: J 286 ASP cc_start: 0.7733 (m-30) cc_final: 0.7237 (t0) REVERT: J 304 GLU cc_start: 0.8012 (tp30) cc_final: 0.7356 (tp30) REVERT: J 331 ARG cc_start: 0.7246 (ttp-170) cc_final: 0.6959 (ttm-80) REVERT: b 46 TYR cc_start: 0.8559 (m-10) cc_final: 0.8164 (m-10) REVERT: a 185 MET cc_start: 0.8129 (ptt) cc_final: 0.7921 (ptt) outliers start: 11 outliers final: 6 residues processed: 177 average time/residue: 0.1235 time to fit residues: 31.6763 Evaluate side-chains 160 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... l 92 HIS ** q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN a 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068964 restraints weight = 53993.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070282 restraints weight = 31862.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070469 restraints weight = 21518.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070688 restraints weight = 18755.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070759 restraints weight = 16961.635| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 15677 Z= 0.309 Angle : 0.741 12.219 22194 Z= 0.377 Chirality : 0.044 0.279 2688 Planarity : 0.006 0.066 1989 Dihedral : 15.490 174.771 4061 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.42 % Allowed : 15.26 % Favored : 82.32 % 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: -0.72 (0.24), residues: 1239 helix: 0.60 (0.23), residues: 504 sheet: -1.30 (0.41), residues: 169 loop : -1.14 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG q 274 TYR 0.020 0.003 TYR q 532 PHE 0.037 0.003 PHE q 408 TRP 0.010 0.002 TRP r 239 HIS 0.006 0.002 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.31 (15677) covalent geometry : angle 0.74091 / 0.38 (22194) hydrogen bonds : bond 0.06108 / 3.69 ( 538) hydrogen bonds : angle 4.65173 / 2.62 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.426 Fit side-chains REVERT: r 250 ASP cc_start: 0.7596 (t0) cc_final: 0.7302 (t0) REVERT: A 47 HIS cc_start: 0.6747 (t70) cc_final: 0.6486 (t-90) REVERT: J 331 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.7020 (ttm-80) REVERT: a 181 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8341 (tm-30) REVERT: a 185 MET cc_start: 0.8088 (ptt) cc_final: 0.7709 (ptm) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.1130 time to fit residues: 29.7458 Evaluate side-chains 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 514 THR Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... q 402 ASN ** w 827 GLN ** 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 = 0.3774 r_free = 0.3774 target = 0.089147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070719 restraints weight = 53472.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072498 restraints weight = 31012.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072754 restraints weight = 19649.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072920 restraints weight = 17093.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072977 restraints weight = 15090.134| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15677 Z= 0.185 Angle : 0.618 10.975 22194 Z= 0.314 Chirality : 0.039 0.240 2688 Planarity : 0.004 0.035 1989 Dihedral : 15.357 176.283 4061 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.06 % Allowed : 18.58 % Favored : 79.35 % 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: -0.59 (0.24), residues: 1239 helix: 0.78 (0.23), residues: 501 sheet: -1.18 (0.41), residues: 167 loop : -1.17 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 130 TYR 0.017 0.002 TYR A 191 PHE 0.019 0.002 PHE q 408 TRP 0.006 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (15677) covalent geometry : angle 0.61794 / 0.31 (22194) hydrogen bonds : bond 0.05057 / 3.06 ( 538) hydrogen bonds : angle 4.41829 / 2.50 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 181 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7940 (mtmm) REVERT: r 250 ASP cc_start: 0.7576 (t0) cc_final: 0.7211 (t0) REVERT: 7 124 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: J 283 GLU cc_start: 0.7142 (tp30) cc_final: 0.6859 (tp30) REVERT: J 286 ASP cc_start: 0.7911 (m-30) cc_final: 0.7344 (t0) REVERT: J 331 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6938 (ttm-80) REVERT: b 46 TYR cc_start: 0.8787 (m-10) cc_final: 0.8344 (m-10) REVERT: a 120 VAL cc_start: 0.8249 (t) cc_final: 0.7941 (t) REVERT: a 181 GLN cc_start: 0.8716 (tm-30) cc_final: 0.7518 (tm-30) REVERT: a 185 MET cc_start: 0.8047 (ptt) cc_final: 0.7710 (ptt) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.1224 time to fit residues: 31.7099 Evaluate side-chains 163 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.090268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071901 restraints weight = 52476.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073614 restraints weight = 30027.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073885 restraints weight = 19063.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074038 restraints weight = 17035.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074092 restraints weight = 15112.292| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15677 Z= 0.141 Angle : 0.581 9.770 22194 Z= 0.295 Chirality : 0.037 0.235 2688 Planarity : 0.004 0.036 1989 Dihedral : 15.239 178.876 4061 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.71 % Allowed : 19.84 % Favored : 78.46 % 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: -0.41 (0.24), residues: 1239 helix: 1.02 (0.24), residues: 496 sheet: -1.15 (0.41), residues: 172 loop : -1.12 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.020 0.001 TYR A 191 PHE 0.015 0.002 PHE q 408 TRP 0.005 0.001 TRP r 239 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15677) covalent geometry : angle 0.58070 / 0.29 (22194) hydrogen bonds : bond 0.04744 / 2.86 ( 538) hydrogen bonds : angle 4.23257 / 2.40 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7455 (t0) cc_final: 0.7042 (t0) REVERT: 7 124 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: A 47 HIS cc_start: 0.6569 (t70) cc_final: 0.6342 (t-90) REVERT: J 266 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6904 (m) REVERT: J 283 GLU cc_start: 0.7086 (tp30) cc_final: 0.6768 (tp30) REVERT: J 286 ASP cc_start: 0.7871 (m-30) cc_final: 0.7289 (t0) REVERT: b 46 TYR cc_start: 0.8530 (m-10) cc_final: 0.8192 (m-10) REVERT: b 139 ILE cc_start: 0.8580 (mm) cc_final: 0.8287 (pt) REVERT: a 120 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.8010 (t) REVERT: a 181 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8369 (tm-30) outliers start: 19 outliers final: 9 residues processed: 179 average time/residue: 0.1289 time to fit residues: 33.6288 Evaluate side-chains 166 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 163 SER Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain r residue 259 LEU Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... l 62 ASN ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN a 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.088327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070037 restraints weight = 53002.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071731 restraints weight = 30508.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071961 restraints weight = 19749.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072139 restraints weight = 17434.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072187 restraints weight = 15372.221| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15677 Z= 0.222 Angle : 0.650 10.188 22194 Z= 0.330 Chirality : 0.040 0.253 2688 Planarity : 0.005 0.054 1989 Dihedral : 15.424 179.775 4061 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.42 % Allowed : 20.29 % Favored : 77.29 % 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: -0.64 (0.24), residues: 1239 helix: 0.79 (0.23), residues: 503 sheet: -1.24 (0.41), residues: 172 loop : -1.24 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 7 27 TYR 0.015 0.002 TYR q 532 PHE 0.025 0.002 PHE q 408 TRP 0.007 0.001 TRP q 302 HIS 0.004 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (15677) covalent geometry : angle 0.65003 / 0.33 (22194) hydrogen bonds : bond 0.05265 / 3.19 ( 538) hydrogen bonds : angle 4.38905 / 2.48 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 227 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: q 403 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: r 250 ASP cc_start: 0.7604 (t0) cc_final: 0.7156 (t0) REVERT: 7 124 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 47 HIS cc_start: 0.6636 (t70) cc_final: 0.6386 (t-90) REVERT: J 283 GLU cc_start: 0.7114 (tp30) cc_final: 0.6794 (tp30) REVERT: J 286 ASP cc_start: 0.7899 (m-30) cc_final: 0.7222 (t0) REVERT: J 331 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7020 (ttm-80) REVERT: b 139 ILE cc_start: 0.8525 (mm) cc_final: 0.8281 (pt) REVERT: a 41 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: a 181 GLN cc_start: 0.8720 (tm-30) cc_final: 0.7410 (tm-30) REVERT: a 185 MET cc_start: 0.8083 (ptt) cc_final: 0.7844 (ptt) outliers start: 27 outliers final: 16 residues processed: 178 average time/residue: 0.1265 time to fit residues: 33.4114 Evaluate side-chains 168 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 163 SER Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 259 LEU Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 136 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070995 restraints weight = 52409.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072369 restraints weight = 29422.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073389 restraints weight = 18445.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073412 restraints weight = 13737.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073406 restraints weight = 13841.738| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15677 Z= 0.125 Angle : 0.591 10.645 22194 Z= 0.298 Chirality : 0.037 0.230 2688 Planarity : 0.004 0.035 1989 Dihedral : 15.277 179.477 4061 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.80 % Allowed : 20.92 % Favored : 77.29 % 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: -0.41 (0.24), residues: 1239 helix: 0.99 (0.23), residues: 498 sheet: -1.03 (0.42), residues: 167 loop : -1.14 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 130 TYR 0.019 0.001 TYR A 191 PHE 0.022 0.002 PHE A 219 TRP 0.004 0.001 TRP q 302 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15677) covalent geometry : angle 0.59124 / 0.30 (22194) hydrogen bonds : bond 0.04778 / 2.88 ( 538) hydrogen bonds : angle 4.22625 / 2.39 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7275 (t0) cc_final: 0.6945 (t0) REVERT: 7 124 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: J 261 LEU cc_start: 0.4551 (mm) cc_final: 0.4262 (mm) REVERT: J 283 GLU cc_start: 0.7045 (tp30) cc_final: 0.6705 (tp30) REVERT: J 286 ASP cc_start: 0.7727 (m-30) cc_final: 0.7141 (t0) REVERT: J 331 ARG cc_start: 0.7252 (ttp-170) cc_final: 0.7036 (ttp-170) REVERT: a 41 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: a 66 CYS cc_start: 0.6232 (t) cc_final: 0.6008 (t) REVERT: a 120 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7979 (t) REVERT: a 181 GLN cc_start: 0.8702 (tm-30) cc_final: 0.7367 (tm-30) outliers start: 20 outliers final: 11 residues processed: 181 average time/residue: 0.1193 time to fit residues: 32.1076 Evaluate side-chains 170 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 163 SER Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain r residue 238 VAL Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS ** b 127 GLN ** 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 = 0.3783 r_free = 0.3783 target = 0.089636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070769 restraints weight = 52428.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071566 restraints weight = 28056.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071863 restraints weight = 18529.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.073009 restraints weight = 16263.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072739 restraints weight = 14326.738| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15677 Z= 0.147 Angle : 0.607 11.044 22194 Z= 0.306 Chirality : 0.038 0.238 2688 Planarity : 0.004 0.036 1989 Dihedral : 15.263 179.324 4061 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.80 % Allowed : 21.36 % Favored : 76.84 % 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: -0.28 (0.24), residues: 1239 helix: 1.14 (0.24), residues: 497 sheet: -0.96 (0.42), residues: 167 loop : -1.11 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.018 0.002 TYR b 46 PHE 0.021 0.002 PHE A 219 TRP 0.005 0.001 TRP q 302 HIS 0.002 0.001 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15677) covalent geometry : angle 0.60742 / 0.31 (22194) hydrogen bonds : bond 0.04820 / 2.92 ( 538) hydrogen bonds : angle 4.20158 / 2.38 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7422 (t0) cc_final: 0.7083 (t0) REVERT: 7 124 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: A 47 HIS cc_start: 0.6764 (t70) cc_final: 0.6505 (t-90) REVERT: J 261 LEU cc_start: 0.4644 (mm) cc_final: 0.4391 (mm) REVERT: J 266 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6895 (m) REVERT: J 283 GLU cc_start: 0.7175 (tp30) cc_final: 0.6759 (tp30) REVERT: J 286 ASP cc_start: 0.7906 (m-30) cc_final: 0.7243 (t0) REVERT: J 310 GLN cc_start: 0.8462 (mp10) cc_final: 0.8005 (mp10) REVERT: J 331 ARG cc_start: 0.7246 (ttp-170) cc_final: 0.6944 (ttm-80) REVERT: a 41 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: a 66 CYS cc_start: 0.6203 (t) cc_final: 0.5884 (t) REVERT: a 185 MET cc_start: 0.8205 (ptt) cc_final: 0.7905 (ptm) outliers start: 20 outliers final: 14 residues processed: 174 average time/residue: 0.1235 time to fit residues: 31.9047 Evaluate side-chains 173 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 163 SER Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 238 VAL Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.089343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070485 restraints weight = 52360.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071295 restraints weight = 27929.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071586 restraints weight = 18459.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072739 restraints weight = 16259.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072465 restraints weight = 14319.607| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15677 Z= 0.160 Angle : 0.619 11.017 22194 Z= 0.313 Chirality : 0.038 0.241 2688 Planarity : 0.004 0.038 1989 Dihedral : 15.290 179.322 4061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.06 % Allowed : 21.36 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1239 helix: 0.95 (0.23), residues: 511 sheet: -0.96 (0.42), residues: 167 loop : -1.15 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.019 0.002 TYR b 46 PHE 0.019 0.002 PHE A 219 TRP 0.005 0.001 TRP q 302 HIS 0.002 0.001 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15677) covalent geometry : angle 0.61880 / 0.31 (22194) hydrogen bonds : bond 0.04913 / 2.98 ( 538) hydrogen bonds : angle 4.22507 / 2.40 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7436 (t0) cc_final: 0.7095 (t0) REVERT: 7 124 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: A 47 HIS cc_start: 0.6789 (t70) cc_final: 0.6549 (t-90) REVERT: J 247 TYR cc_start: 0.4242 (OUTLIER) cc_final: 0.2682 (m-80) REVERT: J 261 LEU cc_start: 0.4820 (mm) cc_final: 0.4570 (mm) REVERT: J 266 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6896 (m) REVERT: J 283 GLU cc_start: 0.7200 (tp30) cc_final: 0.6740 (tp30) REVERT: J 286 ASP cc_start: 0.7906 (m-30) cc_final: 0.7247 (t0) REVERT: J 310 GLN cc_start: 0.8458 (mp10) cc_final: 0.8021 (mp10) REVERT: J 331 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6933 (ttm-80) REVERT: a 41 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: a 66 CYS cc_start: 0.6163 (t) cc_final: 0.5883 (t) REVERT: a 185 MET cc_start: 0.8144 (ptt) cc_final: 0.7890 (ptm) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.1266 time to fit residues: 33.3043 Evaluate side-chains 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 163 SER Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain r residue 238 VAL Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 126 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 129 optimal weight: 0.0670 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.091014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072186 restraints weight = 52151.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073578 restraints weight = 29119.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074498 restraints weight = 18608.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074552 restraints weight = 14501.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074569 restraints weight = 13505.634| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15677 Z= 0.118 Angle : 0.600 11.231 22194 Z= 0.302 Chirality : 0.037 0.232 2688 Planarity : 0.004 0.104 1989 Dihedral : 15.192 179.306 4061 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.62 % Allowed : 22.17 % Favored : 76.21 % 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: -0.40 (0.24), residues: 1239 helix: 1.01 (0.23), residues: 509 sheet: -1.09 (0.42), residues: 157 loop : -1.17 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 122 TYR 0.016 0.001 TYR b 46 PHE 0.021 0.002 PHE A 219 TRP 0.003 0.001 TRP r 239 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15677) covalent geometry : angle 0.60011 / 0.30 (22194) hydrogen bonds : bond 0.04769 / 2.90 ( 538) hydrogen bonds : angle 4.12718 / 2.34 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.64 seconds wall clock time: 41 minutes 40.81 seconds (2500.81 seconds total)