Starting phenix.real_space_refine on Thu Sep 18 07:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7c_24297/09_2025/7r7c_24297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7c_24297/09_2025/7r7c_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_2025/7r7c_24297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2025/7r7c_24297.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2025/7r7c_24297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7c_24297/09_2025/7r7c_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14950 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 4818 Inner-chain residues flagged as termini: ['pdbres=" A 12404 "'] Classifications: {'RNA': 226} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 9, 'rna3p_pur': 103, 'rna3p_pyr': 98} Link IDs: {'rna2p': 25, 'rna3p': 200} Chain breaks: 8 Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain: "r" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "w" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 106 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "7" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 841 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 759 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 3 Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 802 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "b" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Chain: "a" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1696 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 204} Time building chain proxies: 3.61, per 1000 atoms: 0.24 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: 1.31 Conformation dependent library (CDL) restraints added in 561.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.12 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: 3.26 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3356 1.33 - 1.45: 4232 1.45 - 1.57: 7579 1.57 - 1.69: 441 1.69 - 1.81: 69 Bond restraints: 15677 Sorted by residual: bond pdb=" O5' C 12960 " pdb=" C5' C 12960 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" O5' G 12972 " pdb=" C5' G 12972 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.74e+00 bond pdb=" O5' U 1 960 " pdb=" C5' U 1 960 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.56e+00 bond pdb=" C1' G 12972 " pdb=" N9 G 12972 " ideal model delta sigma weight residual 1.475 1.459 0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" CA ILE m 180 " pdb=" CB ILE m 180 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.03e+00 ... (remaining 15672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 21707 1.52 - 3.03: 395 3.03 - 4.55: 68 4.55 - 6.07: 20 6.07 - 7.58: 4 Bond angle restraints: 22194 Sorted by residual: angle pdb=" N GLU 7 53 " pdb=" CA GLU 7 53 " pdb=" CB GLU 7 53 " ideal model delta sigma weight residual 110.12 115.23 -5.11 1.47e+00 4.63e-01 1.21e+01 angle pdb=" C3' C 1 870 " pdb=" O3' C 1 870 " pdb=" P G 1 871 " ideal model delta sigma weight residual 120.20 124.85 -4.65 1.50e+00 4.44e-01 9.60e+00 angle pdb=" C VAL q 538 " pdb=" N ASP q 539 " pdb=" CA ASP q 539 " ideal model delta sigma weight residual 122.19 129.31 -7.12 2.30e+00 1.89e-01 9.59e+00 angle pdb=" O3' C 1 870 " pdb=" C3' C 1 870 " pdb=" C2' C 1 870 " ideal model delta sigma weight residual 113.70 118.19 -4.49 1.50e+00 4.44e-01 8.94e+00 angle pdb=" O3' A 12419 " pdb=" C3' A 12419 " pdb=" C2' A 12419 " ideal model delta sigma weight residual 113.70 118.03 -4.33 1.50e+00 4.44e-01 8.33e+00 ... (remaining 22189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 9125 35.39 - 70.78: 662 70.78 - 106.17: 69 106.17 - 141.57: 4 141.57 - 176.96: 4 Dihedral angle restraints: 9864 sinusoidal: 6179 harmonic: 3685 Sorted by residual: dihedral pdb=" O4' C 1 959 " pdb=" C1' C 1 959 " pdb=" N1 C 1 959 " pdb=" C2 C 1 959 " ideal model delta sinusoidal sigma weight residual 200.00 39.76 160.24 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U 12829 " pdb=" C1' U 12829 " pdb=" N1 U 12829 " pdb=" C2 U 12829 " ideal model delta sinusoidal sigma weight residual 200.00 53.83 146.17 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 200.00 75.85 124.15 1 1.50e+01 4.44e-03 6.66e+01 ... (remaining 9861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2339 0.052 - 0.104: 299 0.104 - 0.156: 48 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA GLN b 127 " pdb=" N GLN b 127 " pdb=" C GLN b 127 " pdb=" CB GLN b 127 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' A 12419 " pdb=" C4' A 12419 " pdb=" O3' A 12419 " pdb=" C2' A 12419 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C3' U 1 960 " pdb=" C4' U 1 960 " pdb=" O3' U 1 960 " pdb=" C2' U 1 960 " both_signs ideal model delta sigma weight residual False -2.48 -2.63 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2685 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12975 " -0.022 2.00e-02 2.50e+03 1.09e-02 2.68e+00 pdb=" N1 U 12975 " 0.022 2.00e-02 2.50e+03 pdb=" C2 U 12975 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 12975 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U 12975 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U 12975 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U 12975 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U 12975 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U 12975 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12451 " -0.022 2.00e-02 2.50e+03 9.30e-03 2.59e+00 pdb=" N9 G 12451 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G 12451 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 12451 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 12451 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 12451 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G 12451 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G 12451 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 12451 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G 12451 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 12451 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 12451 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12974 " -0.020 2.00e-02 2.50e+03 1.04e-02 2.46e+00 pdb=" N1 U 12974 " 0.022 2.00e-02 2.50e+03 pdb=" C2 U 12974 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U 12974 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U 12974 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U 12974 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U 12974 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U 12974 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U 12974 " 0.002 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 627 2.69 - 3.24: 14190 3.24 - 3.79: 25491 3.79 - 4.35: 32741 4.35 - 4.90: 49193 Nonbonded interactions: 122242 Sorted by model distance: nonbonded pdb=" O2' C 1 870 " pdb=" OP1 G 1 871 " model vdw 2.134 3.040 nonbonded pdb=" N2 G 12451 " pdb=" O2 C 12496 " model vdw 2.219 2.496 nonbonded pdb=" OG1 THR A 119 " pdb=" OD1 ASP A 121 " model vdw 2.223 3.040 nonbonded pdb=" O CYS l 69 " pdb=" OG1 THR l 84 " model vdw 2.228 3.040 nonbonded pdb=" O ASP a 150 " pdb=" OG1 THR a 154 " model vdw 2.237 3.040 ... (remaining 122237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15677 Z= 0.111 Angle : 0.530 7.585 22194 Z= 0.276 Chirality : 0.035 0.260 2688 Planarity : 0.003 0.040 1989 Dihedral : 20.675 176.958 7472 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 aren 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 covalent geometry : bond 0.00224 (15677) covalent geometry : angle 0.53047 (22194) hydrogen bonds : bond 0.15800 ( 538) hydrogen bonds : angle 5.83847 ( 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 : 0.515 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: 0.1600 time to fit residues: 46.5658 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 : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 191 GLN r 179 GLN w 837 HIS 7 29 GLN A 195 HIS ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.094420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.075985 restraints weight = 51974.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077341 restraints weight = 28195.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077556 restraints weight = 18430.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077771 restraints weight = 16306.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077792 restraints weight = 14725.799| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15677 Z= 0.120 Angle : 0.564 8.283 22194 Z= 0.285 Chirality : 0.036 0.215 2688 Planarity : 0.004 0.039 1989 Dihedral : 21.933 176.724 4867 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.81 % Allowed : 8.62 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.24), residues: 1239 helix: 1.15 (0.24), residues: 485 sheet: -1.04 (0.44), residues: 150 loop : -0.67 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG r 170 TYR 0.021 0.001 TYR A 191 PHE 0.015 0.002 PHE r 194 TRP 0.002 0.001 TRP a 198 HIS 0.002 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00260 (15677) covalent geometry : angle 0.56399 (22194) hydrogen bonds : bond 0.05322 ( 538) hydrogen bonds : angle 4.56570 ( 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 186 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 367 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7354 (mtt) REVERT: q 541 PHE cc_start: 0.7346 (t80) cc_final: 0.7137 (t80) REVERT: r 195 LEU cc_start: 0.8837 (mp) cc_final: 0.8506 (mt) REVERT: r 244 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7796 (tm-30) REVERT: r 246 THR cc_start: 0.8635 (p) cc_final: 0.8307 (p) REVERT: A 47 HIS cc_start: 0.6464 (t70) cc_final: 0.6236 (t-90) REVERT: A 51 ASP cc_start: 0.7567 (m-30) cc_final: 0.7270 (m-30) REVERT: J 261 LEU cc_start: 0.3842 (mm) cc_final: 0.3578 (mm) REVERT: J 283 GLU cc_start: 0.7204 (tp30) cc_final: 0.6953 (tp30) REVERT: J 286 ASP cc_start: 0.7784 (m-30) cc_final: 0.7289 (t0) REVERT: J 304 GLU cc_start: 0.8018 (tp30) cc_final: 0.7357 (tp30) REVERT: a 120 VAL cc_start: 0.8063 (t) cc_final: 0.7821 (t) REVERT: a 181 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 9 outliers final: 3 residues processed: 181 average time/residue: 0.1468 time to fit residues: 37.8737 Evaluate side-chains 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 367 MET Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 402 ASN r 179 GLN A 165 ASN ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073436 restraints weight = 53159.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075098 restraints weight = 30249.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075337 restraints weight = 19234.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075536 restraints weight = 17152.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075587 restraints weight = 15417.841| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15677 Z= 0.166 Angle : 0.574 9.230 22194 Z= 0.291 Chirality : 0.037 0.239 2688 Planarity : 0.004 0.034 1989 Dihedral : 21.920 175.953 4867 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.26 % Allowed : 12.30 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1239 helix: 1.20 (0.24), residues: 484 sheet: -1.19 (0.43), residues: 157 loop : -0.70 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.017 0.002 TYR A 191 PHE 0.018 0.002 PHE a 157 TRP 0.006 0.001 TRP r 239 HIS 0.005 0.001 HIS q 344 Details of bonding type rmsd covalent geometry : bond 0.00363 (15677) covalent geometry : angle 0.57408 (22194) hydrogen bonds : bond 0.04921 ( 538) hydrogen bonds : angle 4.40938 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7306 (t0) cc_final: 0.7075 (t0) REVERT: A 47 HIS cc_start: 0.6547 (t70) cc_final: 0.6158 (t-90) REVERT: A 51 ASP cc_start: 0.7661 (m-30) cc_final: 0.7396 (m-30) REVERT: A 214 GLU cc_start: 0.6415 (pp20) cc_final: 0.6050 (pp20) REVERT: J 304 GLU cc_start: 0.7934 (tp30) cc_final: 0.7237 (tp30) REVERT: J 331 ARG cc_start: 0.7166 (ttp-170) cc_final: 0.6792 (ttm-80) REVERT: b 46 TYR cc_start: 0.8551 (m-10) cc_final: 0.8159 (m-10) REVERT: a 120 VAL cc_start: 0.8123 (t) cc_final: 0.7875 (t) outliers start: 14 outliers final: 7 residues processed: 175 average time/residue: 0.1437 time to fit residues: 35.7295 Evaluate side-chains 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 278 MET Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3789 r_free = 0.3789 target = 0.090053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071521 restraints weight = 53084.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072772 restraints weight = 31109.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073044 restraints weight = 21000.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073320 restraints weight = 18019.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073386 restraints weight = 16257.886| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15677 Z= 0.204 Angle : 0.616 10.651 22194 Z= 0.313 Chirality : 0.039 0.248 2688 Planarity : 0.005 0.037 1989 Dihedral : 21.964 175.845 4867 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.44 % Allowed : 16.07 % Favored : 82.50 % 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 aren not related in a simple way. whole: -0.27 (0.24), residues: 1239 helix: 0.98 (0.24), residues: 503 sheet: -1.07 (0.42), residues: 167 loop : -0.89 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 122 TYR 0.018 0.002 TYR A 191 PHE 0.021 0.002 PHE q 408 TRP 0.006 0.001 TRP r 239 HIS 0.004 0.001 HIS q 344 Details of bonding type rmsd covalent geometry : bond 0.00446 (15677) covalent geometry : angle 0.61637 (22194) hydrogen bonds : bond 0.05059 ( 538) hydrogen bonds : angle 4.39814 ( 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 173 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7496 (t0) cc_final: 0.7201 (t0) REVERT: A 47 HIS cc_start: 0.6639 (t70) cc_final: 0.6337 (t-90) REVERT: J 283 GLU cc_start: 0.7079 (tp30) cc_final: 0.6769 (tp30) REVERT: J 286 ASP cc_start: 0.7811 (m-30) cc_final: 0.7270 (t0) REVERT: J 304 GLU cc_start: 0.7936 (tp30) cc_final: 0.7088 (tp30) REVERT: J 331 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6887 (ttm-80) REVERT: a 120 VAL cc_start: 0.8029 (t) cc_final: 0.7761 (t) outliers start: 16 outliers final: 12 residues processed: 170 average time/residue: 0.1356 time to fit residues: 33.3343 Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 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: 0.0060 chunk 105 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073199 restraints weight = 52745.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074768 restraints weight = 29375.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075547 restraints weight = 18119.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075703 restraints weight = 14170.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075723 restraints weight = 13920.939| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15677 Z= 0.118 Angle : 0.564 9.139 22194 Z= 0.283 Chirality : 0.036 0.234 2688 Planarity : 0.004 0.034 1989 Dihedral : 21.885 177.045 4867 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.53 % Allowed : 17.24 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.24), residues: 1239 helix: 1.04 (0.24), residues: 501 sheet: -1.21 (0.43), residues: 154 loop : -0.94 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.020 0.001 TYR A 191 PHE 0.018 0.001 PHE r 194 TRP 0.003 0.001 TRP r 239 HIS 0.002 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00258 (15677) covalent geometry : angle 0.56390 (22194) hydrogen bonds : bond 0.04618 ( 538) hydrogen bonds : angle 4.23697 ( 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 189 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: r 181 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7817 (mtmm) REVERT: r 195 LEU cc_start: 0.8687 (mp) cc_final: 0.8427 (mp) REVERT: r 250 ASP cc_start: 0.7346 (t0) cc_final: 0.6999 (t0) REVERT: J 247 TYR cc_start: 0.4096 (OUTLIER) cc_final: 0.2568 (m-80) REVERT: J 261 LEU cc_start: 0.4273 (mm) cc_final: 0.4022 (mm) REVERT: J 266 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6717 (m) REVERT: J 283 GLU cc_start: 0.7084 (tp30) cc_final: 0.6770 (tp30) REVERT: J 286 ASP cc_start: 0.7760 (m-30) cc_final: 0.7213 (t0) REVERT: J 304 GLU cc_start: 0.7955 (tp30) cc_final: 0.7231 (tp30) REVERT: J 331 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6890 (ttm-80) REVERT: a 120 VAL cc_start: 0.8084 (t) cc_final: 0.7844 (t) outliers start: 17 outliers final: 4 residues processed: 185 average time/residue: 0.1420 time to fit residues: 37.5756 Evaluate side-chains 161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 0.0270 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3808 r_free = 0.3808 target = 0.091033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072187 restraints weight = 51856.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072990 restraints weight = 28463.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073635 restraints weight = 18871.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073949 restraints weight = 15930.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073934 restraints weight = 14739.531| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15677 Z= 0.129 Angle : 0.575 10.237 22194 Z= 0.288 Chirality : 0.037 0.237 2688 Planarity : 0.004 0.035 1989 Dihedral : 21.843 177.914 4867 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.35 % Allowed : 19.39 % Favored : 79.26 % 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 aren not related in a simple way. whole: -0.15 (0.24), residues: 1239 helix: 1.19 (0.24), residues: 494 sheet: -1.20 (0.43), residues: 154 loop : -0.87 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 27 TYR 0.020 0.001 TYR A 191 PHE 0.013 0.001 PHE a 190 TRP 0.003 0.001 TRP q 302 HIS 0.002 0.000 HIS a 140 Details of bonding type rmsd covalent geometry : bond 0.00286 (15677) covalent geometry : angle 0.57467 (22194) hydrogen bonds : bond 0.04572 ( 538) hydrogen bonds : angle 4.16226 ( 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 177 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7351 (t0) cc_final: 0.6966 (t0) REVERT: 7 124 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: A 47 HIS cc_start: 0.6445 (t70) cc_final: 0.6236 (t-90) REVERT: J 247 TYR cc_start: 0.3975 (OUTLIER) cc_final: 0.2553 (m-80) REVERT: J 261 LEU cc_start: 0.4089 (mm) cc_final: 0.3881 (mm) REVERT: J 266 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6758 (m) REVERT: J 283 GLU cc_start: 0.7082 (tp30) cc_final: 0.6708 (tp30) REVERT: J 286 ASP cc_start: 0.7686 (m-30) cc_final: 0.7130 (t0) REVERT: J 304 GLU cc_start: 0.7955 (tp30) cc_final: 0.7206 (tp30) REVERT: J 331 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6912 (ttm-80) REVERT: b 139 ILE cc_start: 0.8454 (mm) cc_final: 0.8231 (pt) REVERT: a 63 MET cc_start: 0.6534 (tpp) cc_final: 0.6295 (tpt) REVERT: a 120 VAL cc_start: 0.8179 (t) cc_final: 0.7860 (t) outliers start: 15 outliers final: 8 residues processed: 173 average time/residue: 0.1438 time to fit residues: 35.6157 Evaluate side-chains 166 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 124 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.090292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071008 restraints weight = 51959.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072899 restraints weight = 28839.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.073027 restraints weight = 17429.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073283 restraints weight = 15075.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073354 restraints weight = 13692.786| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15677 Z= 0.151 Angle : 0.581 9.025 22194 Z= 0.293 Chirality : 0.037 0.243 2688 Planarity : 0.004 0.033 1989 Dihedral : 21.862 178.429 4867 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.44 % Allowed : 19.75 % Favored : 78.82 % 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 aren not related in a simple way. whole: -0.17 (0.24), residues: 1239 helix: 1.18 (0.24), residues: 496 sheet: -1.17 (0.42), residues: 157 loop : -0.90 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.019 0.002 TYR A 191 PHE 0.017 0.002 PHE q 408 TRP 0.004 0.001 TRP q 302 HIS 0.002 0.001 HIS q 344 Details of bonding type rmsd covalent geometry : bond 0.00334 (15677) covalent geometry : angle 0.58071 (22194) hydrogen bonds : bond 0.04686 ( 538) hydrogen bonds : angle 4.17334 ( 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 183 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7511 (t0) cc_final: 0.7084 (t0) REVERT: 7 124 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: A 47 HIS cc_start: 0.6664 (t70) cc_final: 0.6413 (t-90) REVERT: J 247 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.2410 (m-80) REVERT: J 266 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6743 (m) REVERT: J 283 GLU cc_start: 0.7176 (tp30) cc_final: 0.6769 (tp30) REVERT: J 286 ASP cc_start: 0.7704 (m-30) cc_final: 0.7096 (t0) REVERT: J 304 GLU cc_start: 0.7946 (tp30) cc_final: 0.7183 (tp30) REVERT: J 310 GLN cc_start: 0.8486 (mp10) cc_final: 0.7954 (mp10) REVERT: J 331 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6960 (ttm-80) REVERT: b 139 ILE cc_start: 0.8502 (mm) cc_final: 0.8289 (pt) REVERT: a 120 VAL cc_start: 0.8113 (t) cc_final: 0.7865 (t) outliers start: 16 outliers final: 10 residues processed: 178 average time/residue: 0.1382 time to fit residues: 35.5457 Evaluate side-chains 171 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 129 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 136 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 0.0870 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3824 r_free = 0.3824 target = 0.091873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072917 restraints weight = 52232.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074310 restraints weight = 29349.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074820 restraints weight = 19044.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075045 restraints weight = 15589.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075091 restraints weight = 14285.475| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15677 Z= 0.111 Angle : 0.568 9.977 22194 Z= 0.285 Chirality : 0.036 0.232 2688 Planarity : 0.003 0.033 1989 Dihedral : 21.789 178.899 4867 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.44 % Allowed : 20.29 % Favored : 78.28 % 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 aren not related in a simple way. whole: -0.11 (0.24), residues: 1239 helix: 1.22 (0.24), residues: 496 sheet: -1.18 (0.42), residues: 159 loop : -0.85 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 130 TYR 0.018 0.001 TYR A 191 PHE 0.013 0.001 PHE a 190 TRP 0.003 0.001 TRP q 302 HIS 0.002 0.000 HIS a 12 Details of bonding type rmsd covalent geometry : bond 0.00242 (15677) covalent geometry : angle 0.56830 (22194) hydrogen bonds : bond 0.04510 ( 538) hydrogen bonds : angle 4.10141 ( 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 189 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 181 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7863 (mttt) REVERT: r 250 ASP cc_start: 0.7258 (t0) cc_final: 0.6842 (t0) REVERT: 7 124 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: A 47 HIS cc_start: 0.6427 (t70) cc_final: 0.6163 (t-90) REVERT: A 202 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7341 (tm-30) REVERT: J 247 TYR cc_start: 0.3673 (OUTLIER) cc_final: 0.2313 (m-80) REVERT: J 283 GLU cc_start: 0.7058 (tp30) cc_final: 0.6686 (tp30) REVERT: J 286 ASP cc_start: 0.7581 (m-30) cc_final: 0.7079 (t0) REVERT: J 304 GLU cc_start: 0.8068 (tp30) cc_final: 0.7322 (tp30) REVERT: J 310 GLN cc_start: 0.8407 (mp10) cc_final: 0.7926 (mp10) REVERT: J 331 ARG cc_start: 0.7098 (ttp-170) cc_final: 0.6803 (ttm-80) REVERT: a 66 CYS cc_start: 0.6288 (t) cc_final: 0.6025 (t) REVERT: a 120 VAL cc_start: 0.8177 (t) cc_final: 0.7929 (t) REVERT: a 185 MET cc_start: 0.8023 (ptt) cc_final: 0.7737 (ptm) outliers start: 16 outliers final: 10 residues processed: 184 average time/residue: 0.1406 time to fit residues: 37.4996 Evaluate side-chains 172 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain a residue 108 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3811 r_free = 0.3811 target = 0.091121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072184 restraints weight = 52451.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073537 restraints weight = 29542.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073839 restraints weight = 19117.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074059 restraints weight = 17248.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074114 restraints weight = 15630.052| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2441 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= 0.137 Angle : 0.588 10.575 22194 Z= 0.296 Chirality : 0.037 0.240 2688 Planarity : 0.004 0.033 1989 Dihedral : 21.777 178.959 4867 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.44 % Allowed : 21.18 % Favored : 77.38 % 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 aren not related in a simple way. whole: -0.11 (0.24), residues: 1239 helix: 1.21 (0.24), residues: 497 sheet: -1.10 (0.43), residues: 157 loop : -0.87 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.020 0.002 TYR b 46 PHE 0.015 0.002 PHE a 190 TRP 0.004 0.001 TRP q 302 HIS 0.004 0.001 HIS a 12 Details of bonding type rmsd covalent geometry : bond 0.00304 (15677) covalent geometry : angle 0.58768 (22194) hydrogen bonds : bond 0.04630 ( 538) hydrogen bonds : angle 4.14050 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7394 (t0) cc_final: 0.7008 (t0) REVERT: 7 124 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: A 47 HIS cc_start: 0.6632 (t70) cc_final: 0.6377 (t-90) REVERT: A 202 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7363 (tm-30) REVERT: J 247 TYR cc_start: 0.3664 (OUTLIER) cc_final: 0.2300 (m-80) REVERT: J 261 LEU cc_start: 0.4249 (mm) cc_final: 0.3985 (mm) REVERT: J 283 GLU cc_start: 0.7129 (tp30) cc_final: 0.6885 (tp30) REVERT: J 304 GLU cc_start: 0.8065 (tp30) cc_final: 0.7313 (tp30) REVERT: J 310 GLN cc_start: 0.8452 (mp10) cc_final: 0.7948 (mp10) REVERT: J 331 ARG cc_start: 0.7174 (ttp-170) cc_final: 0.6890 (ttm-80) REVERT: a 66 CYS cc_start: 0.6254 (t) cc_final: 0.5984 (t) REVERT: a 120 VAL cc_start: 0.8119 (t) cc_final: 0.7890 (t) REVERT: a 185 MET cc_start: 0.8097 (ptt) cc_final: 0.7835 (ptm) outliers start: 16 outliers final: 9 residues processed: 175 average time/residue: 0.1412 time to fit residues: 35.6888 Evaluate side-chains 168 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 30 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 a residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 75 optimal weight: 0.0570 chunk 4 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.089934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070951 restraints weight = 52484.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071940 restraints weight = 28061.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072169 restraints weight = 19414.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072842 restraints weight = 16599.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072777 restraints weight = 14350.813| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15677 Z= 0.177 Angle : 0.624 10.886 22194 Z= 0.316 Chirality : 0.038 0.249 2688 Planarity : 0.004 0.071 1989 Dihedral : 21.850 178.963 4867 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.35 % Allowed : 21.54 % Favored : 77.11 % 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 aren not related in a simple way. whole: -0.20 (0.24), residues: 1239 helix: 1.13 (0.24), residues: 498 sheet: -1.12 (0.43), residues: 157 loop : -0.92 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 122 TYR 0.023 0.002 TYR b 46 PHE 0.018 0.002 PHE q 408 TRP 0.005 0.001 TRP r 239 HIS 0.004 0.001 HIS J 284 Details of bonding type rmsd covalent geometry : bond 0.00393 (15677) covalent geometry : angle 0.62411 (22194) hydrogen bonds : bond 0.04925 ( 538) hydrogen bonds : angle 4.24122 ( 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 177 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7527 (t0) cc_final: 0.7114 (t0) REVERT: 7 124 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 47 HIS cc_start: 0.6658 (t70) cc_final: 0.6436 (t-90) REVERT: J 247 TYR cc_start: 0.3842 (OUTLIER) cc_final: 0.2530 (m-80) REVERT: J 261 LEU cc_start: 0.4605 (mm) cc_final: 0.4333 (mm) REVERT: J 283 GLU cc_start: 0.7202 (tp30) cc_final: 0.6735 (tp30) REVERT: J 286 ASP cc_start: 0.8048 (m-30) cc_final: 0.7339 (t0) REVERT: J 304 GLU cc_start: 0.7937 (tp30) cc_final: 0.7170 (tp30) REVERT: J 310 GLN cc_start: 0.8479 (mp10) cc_final: 0.7968 (mp10) REVERT: a 66 CYS cc_start: 0.6273 (t) cc_final: 0.5953 (t) outliers start: 15 outliers final: 10 residues processed: 171 average time/residue: 0.1325 time to fit residues: 33.1606 Evaluate side-chains 171 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 30 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 a residue 120 VAL Chi-restraints excluded: chain a residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 126 optimal weight: 0.7980 chunk 135 optimal weight: 0.0040 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 129 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 54 GLN ** a 8 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 = 0.3836 r_free = 0.3836 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073618 restraints weight = 51948.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075067 restraints weight = 28836.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075543 restraints weight = 18562.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075752 restraints weight = 15329.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075814 restraints weight = 13949.668| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15677 Z= 0.109 Angle : 0.590 11.042 22194 Z= 0.295 Chirality : 0.036 0.230 2688 Planarity : 0.004 0.033 1989 Dihedral : 21.752 179.339 4867 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.17 % Allowed : 21.72 % Favored : 77.11 % 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 aren not related in a simple way. whole: -0.20 (0.24), residues: 1239 helix: 1.11 (0.24), residues: 503 sheet: -1.15 (0.43), residues: 159 loop : -0.91 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 130 TYR 0.022 0.001 TYR b 46 PHE 0.014 0.001 PHE a 190 TRP 0.003 0.001 TRP q 302 HIS 0.002 0.000 HIS q 450 Details of bonding type rmsd covalent geometry : bond 0.00236 (15677) covalent geometry : angle 0.58959 (22194) hydrogen bonds : bond 0.04702 ( 538) hydrogen bonds : angle 4.11694 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.08 seconds wall clock time: 44 minutes 48.40 seconds (2688.40 seconds total)