Starting phenix.real_space_refine on Sat Sep 12 09:55:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r7c_24297/09_2026/7r7c_24297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7c_24297/09_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_24297/09_2026/7r7c_24297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2026/7r7c_24297.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2026/7r7c_24297.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2026/7r7c_24297.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2026/7r7c_24297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_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-2.2.1-6174/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 Classifications: {'RNAv2': 226} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 9, 'rna3p_pur': 103, 'rna3p_pyr': 98} Link IDs: {'rna2p': 25, 'rna3p': 200} Unresolved chain links: 1 Chain breaks: 8 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 3.39, per 1000 atoms: 0.23 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: 1.20 Conformation dependent library (CDL) restraints added in 665.0 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: 1.85 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: 3.09 Time building geometry restraints manager: 1.65 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=" 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 bond pdb=" C1' G 12972 " pdb=" N9 G 12972 " ideal model delta sigma weight residual 1.478 1.459 0.019 2.00e-02 2.50e+03 9.39e-01 bond pdb=" C GLY l 130 " pdb=" O GLY l 130 " ideal model delta sigma weight residual 1.243 1.234 0.008 9.30e-03 1.16e+04 8.33e-01 bond pdb=" CG GLU 7 53 " pdb=" CD GLU 7 53 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.27e-01 bond pdb=" C GLY 7 96 " pdb=" O GLY 7 96 " ideal model delta sigma weight residual 1.243 1.234 0.008 9.30e-03 1.16e+04 8.27e-01 ... (remaining 15672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 21092 1.52 - 3.03: 885 3.03 - 4.55: 160 4.55 - 6.07: 53 6.07 - 7.58: 4 Bond angle restraints: 22194 Sorted by residual: angle pdb=" C3' C 1 870 " pdb=" O3' C 1 870 " pdb=" P G 1 871 " ideal model delta sigma weight residual 119.70 124.85 -5.15 1.20e+00 6.94e-01 1.84e+01 angle pdb=" C3' U 12417 " pdb=" O3' U 12417 " pdb=" P G 12418 " ideal model delta sigma weight residual 119.70 124.05 -4.35 1.20e+00 6.94e-01 1.31e+01 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' A 12419 " pdb=" O3' A 12419 " pdb=" P C 12420 " ideal model delta sigma weight residual 119.70 123.86 -4.16 1.20e+00 6.94e-01 1.20e+01 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 ... (remaining 22189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.99: 8451 32.99 - 65.97: 554 65.97 - 98.96: 50 98.96 - 131.94: 2 131.94 - 164.93: 1 Dihedral angle restraints: 9058 sinusoidal: 5373 harmonic: 3685 Sorted by residual: dihedral pdb=" C4' A 12486 " pdb=" C3' A 12486 " pdb=" C2' A 12486 " pdb=" C1' A 12486 " ideal model delta sinusoidal sigma weight residual 36.34 -37.72 74.07 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' A 12404 " pdb=" C3' A 12404 " pdb=" C2' A 12404 " pdb=" C1' A 12404 " ideal model delta sinusoidal sigma weight residual 36.34 -37.38 73.72 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A 11129 " pdb=" C3' A 11129 " pdb=" C2' A 11129 " pdb=" C1' A 11129 " ideal model delta sinusoidal sigma weight residual 36.34 -37.09 73.44 1 3.10e+00 1.04e-01 7.14e+02 ... (remaining 9055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2187 0.062 - 0.124: 212 0.124 - 0.186: 13 0.186 - 0.248: 215 0.248 - 0.310: 61 Chirality restraints: 2688 Sorted by residual: chirality pdb=" P G 1 871 " pdb=" OP1 G 1 871 " pdb=" OP2 G 1 871 " pdb=" O5' G 1 871 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' A 12486 " pdb=" C4' A 12486 " pdb=" O3' A 12486 " pdb=" C2' A 12486 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P C 1 959 " pdb=" OP1 C 1 959 " pdb=" OP2 C 1 959 " pdb=" O5' C 1 959 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (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: 0.000 Normalize map: mean=0, sd=1: 6.760 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- 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 : 0.003 0.034 15677 Z= 0.127 Angle : 0.732 7.585 22194 Z= 0.328 Chirality : 0.085 0.310 2688 Planarity : 0.003 0.040 1989 Dihedral : 18.470 164.925 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 0.00262 / 0.13 (15677) covalent geometry : angle 0.73212 / 0.33 (22194) hydrogen bonds : bond 0.15800 / 7.94 ( 538) hydrogen bonds : angle 5.83847 / 2.23 ( 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 : 0.488 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: 0.1481 time to fit residues: 43.6576 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 : 0.488 ------------------------------------------------------------------------------- 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: 5.9990 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: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.094375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075526 restraints weight = 51994.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077156 restraints weight = 29535.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077561 restraints weight = 17814.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077821 restraints weight = 16401.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077908 restraints weight = 15310.197| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1370 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= 0.173 Angle : 0.987 18.269 22194 Z= 0.411 Chirality : 0.080 1.081 2688 Planarity : 0.004 0.054 1989 Dihedral : 17.346 160.124 4061 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.90 % Allowed : 8.89 % Favored : 90.22 % 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: -0.00 (0.24), residues: 1239 helix: 1.16 (0.24), residues: 479 sheet: -0.96 (0.46), residues: 140 loop : -0.65 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 170 TYR 0.019 0.001 TYR A 191 PHE 0.017 0.002 PHE a 190 TRP 0.003 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15677) covalent geometry : angle 0.98713 / 0.41 (22194) hydrogen bonds : bond 0.05644 / 2.84 ( 538) hydrogen bonds : angle 4.60118 / 1.76 ( 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 184 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 367 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: q 541 PHE cc_start: 0.7380 (t80) cc_final: 0.7143 (t80) REVERT: r 244 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7804 (tm-30) REVERT: r 246 THR cc_start: 0.8641 (p) cc_final: 0.8308 (p) REVERT: A 47 HIS cc_start: 0.6451 (t70) cc_final: 0.6215 (t-90) REVERT: A 51 ASP cc_start: 0.7522 (m-30) cc_final: 0.7049 (m-30) REVERT: J 261 LEU cc_start: 0.3641 (mm) cc_final: 0.3391 (mm) REVERT: J 283 GLU cc_start: 0.7179 (tp30) cc_final: 0.6855 (tp30) REVERT: J 286 ASP cc_start: 0.7821 (m-30) cc_final: 0.7299 (t0) REVERT: J 304 GLU cc_start: 0.8012 (tp30) cc_final: 0.7360 (tp30) REVERT: a 181 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7534 (tm-30) outliers start: 10 outliers final: 4 residues processed: 178 average time/residue: 0.1398 time to fit residues: 35.9341 Evaluate side-chains 163 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU 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: 0.8980 chunk 143 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 837 HIS A 165 ASN a 21 ASN ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.088257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069196 restraints weight = 53323.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070429 restraints weight = 31035.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070926 restraints weight = 20769.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071086 restraints weight = 17595.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.071181 restraints weight = 15522.232| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2318 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= 0.301 Angle : 0.979 14.223 22194 Z= 0.423 Chirality : 0.072 0.813 2688 Planarity : 0.006 0.055 1989 Dihedral : 17.334 159.804 4061 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.35 % Allowed : 13.46 % Favored : 85.19 % 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: -0.54 (0.24), residues: 1239 helix: 0.70 (0.23), residues: 495 sheet: -1.24 (0.41), residues: 169 loop : -0.95 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 122 TYR 0.017 0.003 TYR q 322 PHE 0.028 0.003 PHE q 408 TRP 0.011 0.002 TRP r 239 HIS 0.007 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.30 (15677) covalent geometry : angle 0.97943 / 0.42 (22194) hydrogen bonds : bond 0.06183 / 3.12 ( 538) hydrogen bonds : angle 4.71828 / 1.83 ( 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 169 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7370 (t0) cc_final: 0.7149 (t0) REVERT: A 47 HIS cc_start: 0.6838 (t70) cc_final: 0.6602 (t-90) REVERT: A 214 GLU cc_start: 0.6625 (pp20) cc_final: 0.6120 (pp20) REVERT: J 251 LEU cc_start: 0.3538 (OUTLIER) cc_final: 0.3203 (mm) REVERT: J 331 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6942 (ttm-80) outliers start: 15 outliers final: 8 residues processed: 165 average time/residue: 0.1354 time to fit residues: 32.1510 Evaluate side-chains 148 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... q 402 ASN ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.088844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070194 restraints weight = 52661.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071200 restraints weight = 29408.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071347 restraints weight = 20180.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071683 restraints weight = 17318.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071765 restraints weight = 15872.400| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15677 Z= 0.221 Angle : 0.879 12.423 22194 Z= 0.378 Chirality : 0.066 0.679 2688 Planarity : 0.005 0.037 1989 Dihedral : 17.208 171.840 4061 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.06 % Allowed : 15.89 % Favored : 82.05 % 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: -0.54 (0.24), residues: 1239 helix: 0.83 (0.23), residues: 505 sheet: -1.16 (0.41), residues: 167 loop : -1.15 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 274 TYR 0.012 0.002 TYR q 516 PHE 0.021 0.002 PHE q 408 TRP 0.009 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (15677) covalent geometry : angle 0.87884 / 0.38 (22194) hydrogen bonds : bond 0.05593 / 2.82 ( 538) hydrogen bonds : angle 4.49379 / 1.74 ( 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 177 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7521 (t0) cc_final: 0.7184 (t0) REVERT: A 214 GLU cc_start: 0.7168 (pp20) cc_final: 0.6625 (pp20) REVERT: J 283 GLU cc_start: 0.7169 (tp30) cc_final: 0.6802 (tp30) REVERT: J 286 ASP cc_start: 0.8014 (m-30) cc_final: 0.7328 (t0) REVERT: J 331 ARG cc_start: 0.7218 (ttp-170) cc_final: 0.6923 (ttm-80) REVERT: b 46 TYR cc_start: 0.8727 (m-10) cc_final: 0.8318 (m-10) REVERT: b 139 ILE cc_start: 0.8689 (mm) cc_final: 0.8450 (pt) outliers start: 23 outliers final: 11 residues processed: 171 average time/residue: 0.1281 time to fit residues: 32.3214 Evaluate side-chains 153 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL 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 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 105 THR 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 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.088976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069777 restraints weight = 52816.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071755 restraints weight = 29878.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071865 restraints weight = 17477.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072076 restraints weight = 14976.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072141 restraints weight = 13733.790| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15677 Z= 0.196 Angle : 0.864 11.324 22194 Z= 0.370 Chirality : 0.063 0.619 2688 Planarity : 0.004 0.036 1989 Dihedral : 17.122 177.212 4061 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.71 % Allowed : 18.13 % Favored : 80.16 % 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: -0.51 (0.24), residues: 1239 helix: 0.88 (0.23), residues: 504 sheet: -1.17 (0.41), residues: 167 loop : -1.16 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 27 TYR 0.014 0.002 TYR A 191 PHE 0.019 0.002 PHE q 408 TRP 0.008 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (15677) covalent geometry : angle 0.86373 / 0.37 (22194) hydrogen bonds : bond 0.05591 / 2.82 ( 538) hydrogen bonds : angle 4.38156 / 1.69 ( 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 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7499 (t0) cc_final: 0.7143 (t0) REVERT: 7 53 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: 7 124 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: A 47 HIS cc_start: 0.6683 (t70) cc_final: 0.6430 (t-90) REVERT: A 214 GLU cc_start: 0.7397 (pp20) cc_final: 0.7045 (pp20) REVERT: J 261 LEU cc_start: 0.4357 (mm) cc_final: 0.4150 (mm) REVERT: J 266 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6629 (m) REVERT: J 283 GLU cc_start: 0.7191 (tp30) cc_final: 0.6826 (tp30) REVERT: J 286 ASP cc_start: 0.7918 (m-30) cc_final: 0.7283 (t0) REVERT: J 331 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6975 (ttm-80) REVERT: b 46 TYR cc_start: 0.8546 (m-10) cc_final: 0.8293 (m-10) REVERT: b 139 ILE cc_start: 0.8647 (mm) cc_final: 0.8430 (pt) REVERT: a 174 MET cc_start: 0.7511 (pmm) cc_final: 0.7307 (pmm) outliers start: 19 outliers final: 14 residues processed: 169 average time/residue: 0.1267 time to fit residues: 31.8716 Evaluate side-chains 163 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 127 GLU 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 q residue 514 THR Chi-restraints excluded: chain r residue 259 LEU Chi-restraints excluded: chain 7 residue 53 GLU 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 210 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 114 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 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 = 0.3837 r_free = 0.3837 target = 0.092499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073632 restraints weight = 51631.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075796 restraints weight = 29052.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075827 restraints weight = 16921.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076035 restraints weight = 14433.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076030 restraints weight = 13471.589| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2805 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= 0.127 Angle : 0.793 11.222 22194 Z= 0.340 Chirality : 0.059 0.445 2688 Planarity : 0.004 0.035 1989 Dihedral : 16.866 175.935 4061 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.80 % Allowed : 19.30 % Favored : 78.90 % 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: -0.35 (0.24), residues: 1239 helix: 1.07 (0.24), residues: 504 sheet: -1.26 (0.42), residues: 159 loop : -1.07 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 27 TYR 0.017 0.001 TYR A 191 PHE 0.027 0.002 PHE A 219 TRP 0.002 0.000 TRP a 198 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (15677) covalent geometry : angle 0.79321 / 0.34 (22194) hydrogen bonds : bond 0.05309 / 2.68 ( 538) hydrogen bonds : angle 4.16404 / 1.60 ( 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 197 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: q 229 ASP cc_start: 0.8143 (m-30) cc_final: 0.7902 (m-30) REVERT: r 181 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7598 (mtmm) REVERT: r 195 LEU cc_start: 0.8673 (mp) cc_final: 0.8302 (mp) REVERT: r 250 ASP cc_start: 0.7190 (t0) cc_final: 0.6821 (t0) REVERT: 7 53 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: 7 124 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 47 HIS cc_start: 0.6551 (t70) cc_final: 0.6238 (t-90) REVERT: A 51 ASP cc_start: 0.7861 (m-30) cc_final: 0.7340 (m-30) REVERT: J 247 TYR cc_start: 0.3998 (OUTLIER) cc_final: 0.2467 (m-80) REVERT: J 266 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6945 (m) REVERT: J 283 GLU cc_start: 0.7095 (tp30) cc_final: 0.6690 (tp30) REVERT: J 286 ASP cc_start: 0.7741 (m-30) cc_final: 0.7172 (t0) REVERT: J 304 GLU cc_start: 0.7952 (tp30) cc_final: 0.7443 (tp30) REVERT: J 331 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6973 (ttm-80) REVERT: a 174 MET cc_start: 0.7220 (pmm) cc_final: 0.6866 (pmm) outliers start: 20 outliers final: 6 residues processed: 192 average time/residue: 0.1282 time to fit residues: 36.3804 Evaluate side-chains 169 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain 7 residue 53 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... l 62 ASN ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.089586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070388 restraints weight = 52174.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072319 restraints weight = 29335.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072428 restraints weight = 17295.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072658 restraints weight = 15020.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072722 restraints weight = 13639.926| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15677 Z= 0.202 Angle : 0.848 10.135 22194 Z= 0.365 Chirality : 0.061 0.433 2688 Planarity : 0.004 0.036 1989 Dihedral : 16.859 175.359 4061 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.71 % Allowed : 20.38 % Favored : 77.92 % 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: -0.31 (0.24), residues: 1239 helix: 1.04 (0.24), residues: 503 sheet: -1.04 (0.42), residues: 167 loop : -1.04 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 122 TYR 0.016 0.002 TYR q 532 PHE 0.019 0.002 PHE q 408 TRP 0.007 0.001 TRP r 239 HIS 0.003 0.001 HIS q 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (15677) covalent geometry : angle 0.84788 / 0.37 (22194) hydrogen bonds : bond 0.05625 / 2.84 ( 538) hydrogen bonds : angle 4.25719 / 1.63 ( 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: 19 poor density : 163 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 229 ASP cc_start: 0.8171 (m-30) cc_final: 0.7964 (m-30) REVERT: q 403 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: r 181 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7684 (mtmm) REVERT: r 250 ASP cc_start: 0.7535 (t0) cc_final: 0.7131 (t0) REVERT: 7 124 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: J 247 TYR cc_start: 0.4204 (OUTLIER) cc_final: 0.2709 (m-80) REVERT: J 282 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7613 (t70) REVERT: J 283 GLU cc_start: 0.7160 (tp30) cc_final: 0.6896 (tp30) REVERT: J 331 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6913 (ttm-80) REVERT: a 174 MET cc_start: 0.7302 (pmm) cc_final: 0.7007 (pmm) outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 0.1291 time to fit residues: 33.6924 Evaluate side-chains 166 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain 7 residue 30 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 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 282 ASP Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 136 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 45 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 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 = 0.3804 r_free = 0.3804 target = 0.090636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071601 restraints weight = 52459.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073425 restraints weight = 28857.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073558 restraints weight = 17635.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073839 restraints weight = 14914.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073888 restraints weight = 13535.741| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3012 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= 0.146 Angle : 0.810 9.691 22194 Z= 0.349 Chirality : 0.059 0.430 2688 Planarity : 0.004 0.035 1989 Dihedral : 16.817 176.364 4061 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.89 % Allowed : 20.92 % Favored : 77.20 % 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: 0.97 (0.23), residues: 505 sheet: -1.20 (0.42), residues: 157 loop : -1.08 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG q 274 TYR 0.017 0.002 TYR A 191 PHE 0.020 0.002 PHE A 219 TRP 0.005 0.001 TRP r 239 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (15677) covalent geometry : angle 0.81048 / 0.35 (22194) hydrogen bonds : bond 0.05587 / 2.82 ( 538) hydrogen bonds : angle 4.22364 / 1.62 ( 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 181 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 403 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: r 195 LEU cc_start: 0.8747 (mp) cc_final: 0.8400 (mp) REVERT: r 250 ASP cc_start: 0.7367 (t0) cc_final: 0.7057 (t0) REVERT: 7 124 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: A 47 HIS cc_start: 0.6684 (t70) cc_final: 0.5888 (t-90) REVERT: J 247 TYR cc_start: 0.4011 (OUTLIER) cc_final: 0.2456 (m-80) REVERT: J 261 LEU cc_start: 0.4311 (mm) cc_final: 0.4044 (mm) REVERT: J 283 GLU cc_start: 0.7173 (tp30) cc_final: 0.6712 (tp30) REVERT: J 286 ASP cc_start: 0.7831 (m-30) cc_final: 0.7177 (t0) REVERT: J 304 GLU cc_start: 0.7951 (tp30) cc_final: 0.7406 (tp30) REVERT: J 310 GLN cc_start: 0.8425 (mp10) cc_final: 0.7945 (mp10) REVERT: a 41 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: a 66 CYS cc_start: 0.6179 (t) cc_final: 0.5868 (t) REVERT: a 174 MET cc_start: 0.7292 (pmm) cc_final: 0.7020 (pmm) REVERT: a 185 MET cc_start: 0.8183 (ptt) cc_final: 0.7930 (ptm) outliers start: 21 outliers final: 10 residues processed: 175 average time/residue: 0.1282 time to fit residues: 32.9502 Evaluate side-chains 172 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain 7 residue 30 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 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 41 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 76 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 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 = 0.3807 r_free = 0.3807 target = 0.090777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071755 restraints weight = 52227.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073685 restraints weight = 29460.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073812 restraints weight = 17838.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074044 restraints weight = 15409.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074117 restraints weight = 13909.904| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15677 Z= 0.149 Angle : 0.817 9.899 22194 Z= 0.353 Chirality : 0.059 0.447 2688 Planarity : 0.004 0.035 1989 Dihedral : 16.781 176.680 4061 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.53 % Allowed : 21.27 % Favored : 77.20 % 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: -0.42 (0.24), residues: 1239 helix: 0.92 (0.23), residues: 505 sheet: -1.17 (0.42), residues: 157 loop : -1.07 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 331 TYR 0.018 0.002 TYR q 227 PHE 0.019 0.002 PHE A 219 TRP 0.006 0.001 TRP r 239 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15677) covalent geometry : angle 0.81732 / 0.35 (22194) hydrogen bonds : bond 0.05660 / 2.85 ( 538) hydrogen bonds : angle 4.24520 / 1.62 ( 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 177 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 403 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: r 195 LEU cc_start: 0.8697 (mp) cc_final: 0.8491 (mp) REVERT: r 250 ASP cc_start: 0.7308 (t0) cc_final: 0.6992 (t0) REVERT: 7 124 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: A 47 HIS cc_start: 0.6657 (t70) cc_final: 0.5901 (t-90) REVERT: J 247 TYR cc_start: 0.3876 (OUTLIER) cc_final: 0.2343 (m-80) REVERT: J 261 LEU cc_start: 0.4642 (mm) cc_final: 0.4418 (mm) REVERT: J 283 GLU cc_start: 0.7101 (tp30) cc_final: 0.6685 (tp30) REVERT: J 286 ASP cc_start: 0.7730 (m-30) cc_final: 0.7147 (t0) REVERT: J 304 GLU cc_start: 0.7954 (tp30) cc_final: 0.7416 (tp30) REVERT: J 310 GLN cc_start: 0.8403 (mp10) cc_final: 0.7952 (mp10) REVERT: J 331 ARG cc_start: 0.7214 (ttp-170) cc_final: 0.6809 (ttm-80) REVERT: a 41 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: a 66 CYS cc_start: 0.6115 (t) cc_final: 0.5880 (t) REVERT: a 171 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7189 (p0) outliers start: 17 outliers final: 10 residues processed: 171 average time/residue: 0.1262 time to fit residues: 31.9442 Evaluate side-chains 172 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain 7 residue 30 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 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 171 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 124 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 75 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 69 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.093870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075030 restraints weight = 51835.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076959 restraints weight = 28916.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077143 restraints weight = 17522.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077403 restraints weight = 14749.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077467 restraints weight = 13423.621| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15677 Z= 0.124 Angle : 0.791 10.141 22194 Z= 0.343 Chirality : 0.058 0.371 2688 Planarity : 0.004 0.035 1989 Dihedral : 16.586 176.297 4061 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.17 % Allowed : 22.08 % Favored : 76.75 % 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: 0.89 (0.23), residues: 509 sheet: -1.10 (0.42), residues: 159 loop : -1.05 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 331 TYR 0.020 0.001 TYR b 46 PHE 0.021 0.001 PHE A 219 TRP 0.003 0.000 TRP q 302 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15677) covalent geometry : angle 0.79115 / 0.34 (22194) hydrogen bonds : bond 0.05695 / 2.87 ( 538) hydrogen bonds : angle 4.16732 / 1.59 ( 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 192 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 403 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (m-10) REVERT: r 195 LEU cc_start: 0.8546 (mp) cc_final: 0.8165 (mp) REVERT: r 250 ASP cc_start: 0.7206 (t0) cc_final: 0.6831 (t0) REVERT: 7 124 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: A 47 HIS cc_start: 0.6528 (t70) cc_final: 0.5738 (t-90) REVERT: J 247 TYR cc_start: 0.3515 (OUTLIER) cc_final: 0.2154 (m-80) REVERT: J 283 GLU cc_start: 0.7052 (tp30) cc_final: 0.6610 (tp30) REVERT: J 286 ASP cc_start: 0.7718 (m-30) cc_final: 0.7158 (t0) REVERT: J 304 GLU cc_start: 0.8161 (tp30) cc_final: 0.7505 (tp30) REVERT: J 310 GLN cc_start: 0.8475 (mp10) cc_final: 0.7985 (mp10) REVERT: J 331 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6864 (ttm-80) REVERT: a 41 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: a 66 CYS cc_start: 0.6129 (t) cc_final: 0.5845 (t) REVERT: a 185 MET cc_start: 0.8063 (ptt) cc_final: 0.7794 (ptm) outliers start: 13 outliers final: 7 residues processed: 188 average time/residue: 0.1356 time to fit residues: 37.2216 Evaluate side-chains 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain 7 residue 30 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 333 THR Chi-restraints excluded: chain a residue 41 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070914 restraints weight = 52728.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072336 restraints weight = 29649.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073194 restraints weight = 18728.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073282 restraints weight = 14541.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073428 restraints weight = 14095.003| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15677 Z= 0.208 Angle : 0.854 9.230 22194 Z= 0.370 Chirality : 0.060 0.412 2688 Planarity : 0.005 0.057 1989 Dihedral : 16.689 176.300 4061 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.62 % Allowed : 21.81 % 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: -0.49 (0.24), residues: 1239 helix: 0.84 (0.23), residues: 511 sheet: -1.17 (0.42), residues: 157 loop : -1.11 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 274 TYR 0.023 0.002 TYR b 46 PHE 0.027 0.002 PHE b 45 TRP 0.004 0.001 TRP q 302 HIS 0.003 0.001 HIS q 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (15677) covalent geometry : angle 0.85410 / 0.37 (22194) hydrogen bonds : bond 0.05990 / 3.02 ( 538) hydrogen bonds : angle 4.28500 / 1.64 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.39 seconds wall clock time: 44 minutes 2.45 seconds (2642.45 seconds total)