Starting phenix.real_space_refine on Tue Dec 31 07:26:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7c_24297/12_2024/7r7c_24297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7c_24297/12_2024/7r7c_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_24297/12_2024/7r7c_24297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7c_24297/12_2024/7r7c_24297.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7c_24297/12_2024/7r7c_24297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7c_24297/12_2024/7r7c_24297.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.49, per 1000 atoms: 0.63 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: 3.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 5.96 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: 6.64 Time building geometry restraints manager: 4.27 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 39.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.020 ------------------------------------------------------------------------------- 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= 0.144 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 : 11.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP r 239 HIS 0.002 0.000 HIS q 450 PHE 0.023 0.001 PHE q 253 TYR 0.013 0.001 TYR q 516 ARG 0.008 0.000 ARG b 130 *********************** 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 : 1.293 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: 0.3337 time to fit residues: 96.6423 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 : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 113 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.6014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15677 Z= 0.173 Angle : 0.570 8.491 22194 Z= 0.287 Chirality : 0.036 0.214 2688 Planarity : 0.004 0.040 1989 Dihedral : 21.919 176.659 4867 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.90 % Allowed : 8.44 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1239 helix: 1.16 (0.24), residues: 484 sheet: -1.03 (0.45), residues: 143 loop : -0.67 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP r 239 HIS 0.003 0.001 HIS A 58 PHE 0.016 0.002 PHE r 194 TYR 0.019 0.001 TYR A 191 ARG 0.003 0.000 ARG r 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 195 LEU cc_start: 0.8803 (mp) cc_final: 0.8434 (mt) REVERT: r 244 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7828 (tm-30) REVERT: r 246 THR cc_start: 0.8606 (p) cc_final: 0.8276 (p) REVERT: A 47 HIS cc_start: 0.6222 (t70) cc_final: 0.6004 (t-90) REVERT: A 51 ASP cc_start: 0.7367 (m-30) cc_final: 0.7110 (m-30) REVERT: J 261 LEU cc_start: 0.3932 (mm) cc_final: 0.3679 (mm) REVERT: J 286 ASP cc_start: 0.7676 (m-30) cc_final: 0.7240 (t0) REVERT: J 304 GLU cc_start: 0.7988 (tp30) cc_final: 0.7373 (tp30) REVERT: a 120 VAL cc_start: 0.8119 (t) cc_final: 0.7902 (t) REVERT: a 181 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7445 (tm-30) outliers start: 10 outliers final: 4 residues processed: 183 average time/residue: 0.3193 time to fit residues: 83.7082 Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain m residue 176 ASN 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 73 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 92 HIS q 402 ASN r 179 GLN ** 7 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15677 Z= 0.291 Angle : 0.614 10.883 22194 Z= 0.313 Chirality : 0.039 0.249 2688 Planarity : 0.005 0.038 1989 Dihedral : 22.001 175.485 4867 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.44 % Allowed : 13.64 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1239 helix: 1.01 (0.24), residues: 494 sheet: -0.99 (0.42), residues: 167 loop : -0.74 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP r 239 HIS 0.006 0.001 HIS q 344 PHE 0.021 0.002 PHE q 408 TYR 0.018 0.002 TYR A 191 ARG 0.005 0.001 ARG q 274 *********************** 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 176 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.521 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7339 (t0) cc_final: 0.7079 (t0) REVERT: J 251 LEU cc_start: 0.3822 (OUTLIER) cc_final: 0.3584 (mm) REVERT: J 261 LEU cc_start: 0.4486 (mm) cc_final: 0.4281 (mm) REVERT: J 304 GLU cc_start: 0.7912 (tp30) cc_final: 0.7109 (tp30) REVERT: J 331 ARG cc_start: 0.7201 (ttp-170) cc_final: 0.6856 (ttm-80) REVERT: b 46 TYR cc_start: 0.8516 (m-10) cc_final: 0.8261 (m-10) REVERT: a 120 VAL cc_start: 0.8162 (t) cc_final: 0.7907 (t) outliers start: 16 outliers final: 7 residues processed: 171 average time/residue: 0.3090 time to fit residues: 75.4421 Evaluate side-chains 151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 367 MET Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15677 Z= 0.166 Angle : 0.556 7.721 22194 Z= 0.281 Chirality : 0.036 0.231 2688 Planarity : 0.004 0.033 1989 Dihedral : 21.883 176.446 4867 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.62 % Allowed : 16.25 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1239 helix: 1.12 (0.24), residues: 493 sheet: -1.15 (0.44), residues: 154 loop : -0.85 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP r 239 HIS 0.003 0.000 HIS J 284 PHE 0.015 0.001 PHE r 194 TYR 0.022 0.001 TYR A 191 ARG 0.007 0.000 ARG a 122 *********************** 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 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: q 541 PHE cc_start: 0.7663 (t80) cc_final: 0.7439 (t80) REVERT: r 250 ASP cc_start: 0.7283 (t0) cc_final: 0.6958 (t0) REVERT: A 47 HIS cc_start: 0.6293 (t70) cc_final: 0.5990 (t-90) REVERT: J 283 GLU cc_start: 0.6967 (tp30) cc_final: 0.6447 (tp30) REVERT: J 286 ASP cc_start: 0.7722 (m-30) cc_final: 0.7260 (t0) REVERT: J 304 GLU cc_start: 0.7946 (tp30) cc_final: 0.7255 (tp30) REVERT: J 331 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6886 (ttm-80) REVERT: a 120 VAL cc_start: 0.8111 (t) cc_final: 0.7859 (t) outliers start: 18 outliers final: 7 residues processed: 183 average time/residue: 0.2888 time to fit residues: 77.1240 Evaluate side-chains 161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain J residue 247 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1976 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= 0.179 Angle : 0.564 10.150 22194 Z= 0.282 Chirality : 0.036 0.235 2688 Planarity : 0.004 0.034 1989 Dihedral : 21.839 177.245 4867 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.53 % Allowed : 17.59 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1239 helix: 1.20 (0.24), residues: 491 sheet: -1.13 (0.43), residues: 154 loop : -0.84 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP q 302 HIS 0.002 0.000 HIS q 344 PHE 0.019 0.001 PHE r 194 TYR 0.021 0.001 TYR A 191 ARG 0.004 0.000 ARG b 130 *********************** 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 180 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7381 (t0) cc_final: 0.7038 (t0) REVERT: 7 53 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6807 (mm-30) REVERT: A 47 HIS cc_start: 0.6256 (t70) cc_final: 0.5899 (t-90) REVERT: J 247 TYR cc_start: 0.4054 (OUTLIER) cc_final: 0.2564 (m-80) REVERT: J 283 GLU cc_start: 0.6980 (tp30) cc_final: 0.6417 (tp30) REVERT: J 286 ASP cc_start: 0.7712 (m-30) cc_final: 0.7212 (t0) REVERT: J 304 GLU cc_start: 0.8053 (tp30) cc_final: 0.7374 (tp30) REVERT: J 331 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.6973 (ttm-80) REVERT: b 46 TYR cc_start: 0.8282 (m-10) cc_final: 0.8068 (m-10) REVERT: a 120 VAL cc_start: 0.8041 (t) cc_final: 0.7782 (t) outliers start: 17 outliers final: 9 residues processed: 175 average time/residue: 0.3493 time to fit residues: 88.1678 Evaluate side-chains 164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 53 GLU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 140 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2070 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= 0.153 Angle : 0.549 8.751 22194 Z= 0.275 Chirality : 0.036 0.233 2688 Planarity : 0.004 0.033 1989 Dihedral : 21.783 177.980 4867 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.53 % Allowed : 18.85 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1239 helix: 1.22 (0.24), residues: 492 sheet: -1.08 (0.43), residues: 154 loop : -0.81 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP l 98 HIS 0.002 0.000 HIS a 140 PHE 0.015 0.001 PHE r 194 TYR 0.020 0.001 TYR A 191 ARG 0.003 0.000 ARG b 130 *********************** 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 192 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 181 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7568 (mtmm) REVERT: r 195 LEU cc_start: 0.8556 (mp) cc_final: 0.8283 (mp) REVERT: r 250 ASP cc_start: 0.7368 (t0) cc_final: 0.6998 (t0) REVERT: 7 124 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: A 47 HIS cc_start: 0.6258 (t70) cc_final: 0.5869 (t-90) REVERT: J 247 TYR cc_start: 0.3967 (OUTLIER) cc_final: 0.2484 (m-80) REVERT: J 261 LEU cc_start: 0.3830 (mm) cc_final: 0.3608 (mm) REVERT: J 266 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6679 (m) REVERT: J 283 GLU cc_start: 0.6922 (tp30) cc_final: 0.6341 (tp30) REVERT: J 286 ASP cc_start: 0.7479 (m-30) cc_final: 0.6950 (t0) REVERT: J 304 GLU cc_start: 0.8051 (tp30) cc_final: 0.7319 (tp30) REVERT: J 310 GLN cc_start: 0.8358 (mp10) cc_final: 0.7861 (mp10) REVERT: J 331 ARG cc_start: 0.7204 (ttp-170) cc_final: 0.6924 (ttm-80) REVERT: a 120 VAL cc_start: 0.8162 (t) cc_final: 0.7836 (t) outliers start: 17 outliers final: 8 residues processed: 187 average time/residue: 0.3341 time to fit residues: 91.9746 Evaluate side-chains 170 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 266 VAL Chi-restraints excluded: chain a residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 0.0040 chunk 139 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2171 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= 0.160 Angle : 0.566 10.633 22194 Z= 0.281 Chirality : 0.036 0.236 2688 Planarity : 0.004 0.032 1989 Dihedral : 21.756 178.261 4867 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.80 % Allowed : 19.48 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1239 helix: 1.15 (0.24), residues: 502 sheet: -0.96 (0.43), residues: 159 loop : -0.84 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP l 98 HIS 0.002 0.000 HIS a 140 PHE 0.014 0.001 PHE r 194 TYR 0.014 0.001 TYR A 191 ARG 0.003 0.000 ARG b 130 *********************** 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 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 181 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7564 (mtmm) REVERT: r 195 LEU cc_start: 0.8687 (mp) cc_final: 0.8478 (mp) REVERT: r 250 ASP cc_start: 0.7378 (t0) cc_final: 0.6981 (t0) REVERT: 7 124 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7162 (tp30) REVERT: A 47 HIS cc_start: 0.6221 (t70) cc_final: 0.5858 (t-90) REVERT: J 247 TYR cc_start: 0.3727 (OUTLIER) cc_final: 0.2264 (m-80) REVERT: J 261 LEU cc_start: 0.3963 (mm) cc_final: 0.3748 (mm) REVERT: J 266 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6731 (m) REVERT: J 283 GLU cc_start: 0.6884 (tp30) cc_final: 0.6288 (tp30) REVERT: J 286 ASP cc_start: 0.7500 (m-30) cc_final: 0.6985 (t0) REVERT: J 304 GLU cc_start: 0.8057 (tp30) cc_final: 0.7326 (tp30) REVERT: J 310 GLN cc_start: 0.8365 (mp10) cc_final: 0.7870 (mp10) REVERT: J 331 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6916 (ttm-80) REVERT: a 120 VAL cc_start: 0.8118 (t) cc_final: 0.7804 (t) outliers start: 20 outliers final: 12 residues processed: 182 average time/residue: 0.3061 time to fit residues: 81.1376 Evaluate side-chains 174 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 J residue 266 VAL Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15677 Z= 0.245 Angle : 0.612 10.188 22194 Z= 0.308 Chirality : 0.038 0.253 2688 Planarity : 0.004 0.032 1989 Dihedral : 21.860 178.164 4867 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.97 % Allowed : 19.48 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1239 helix: 1.10 (0.24), residues: 503 sheet: -0.95 (0.43), residues: 157 loop : -0.91 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP r 239 HIS 0.003 0.001 HIS a 140 PHE 0.020 0.002 PHE q 408 TYR 0.017 0.002 TYR A 203 ARG 0.005 0.000 ARG q 274 *********************** 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 183 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7543 (t0) cc_final: 0.7164 (t0) REVERT: 7 124 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: J 247 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.2347 (m-80) REVERT: J 266 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6688 (m) REVERT: J 283 GLU cc_start: 0.6920 (tp30) cc_final: 0.6648 (tp30) REVERT: J 304 GLU cc_start: 0.7954 (tp30) cc_final: 0.7180 (tp30) REVERT: J 310 GLN cc_start: 0.8393 (mp10) cc_final: 0.7948 (mp10) REVERT: J 331 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6933 (ttm-80) REVERT: a 120 VAL cc_start: 0.8182 (t) cc_final: 0.7946 (t) REVERT: a 185 MET cc_start: 0.7857 (ptt) cc_final: 0.7553 (ptm) outliers start: 22 outliers final: 15 residues processed: 176 average time/residue: 0.3096 time to fit residues: 78.9359 Evaluate side-chains 173 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 r residue 193 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain J residue 247 TYR Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2437 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= 0.163 Angle : 0.586 10.840 22194 Z= 0.291 Chirality : 0.036 0.232 2688 Planarity : 0.004 0.054 1989 Dihedral : 21.770 178.665 4867 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.62 % Allowed : 20.02 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1239 helix: 1.17 (0.24), residues: 497 sheet: -1.06 (0.43), residues: 157 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP r 239 HIS 0.003 0.000 HIS A 47 PHE 0.014 0.001 PHE a 190 TYR 0.023 0.001 TYR A 191 ARG 0.004 0.000 ARG b 130 *********************** 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 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7347 (t0) cc_final: 0.6915 (t0) REVERT: 7 124 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 47 HIS cc_start: 0.6265 (t70) cc_final: 0.5533 (t-90) REVERT: J 247 TYR cc_start: 0.3465 (OUTLIER) cc_final: 0.2298 (m-80) REVERT: J 283 GLU cc_start: 0.6844 (tp30) cc_final: 0.6280 (tp30) REVERT: J 286 ASP cc_start: 0.7617 (m-30) cc_final: 0.7068 (t0) REVERT: J 304 GLU cc_start: 0.8045 (tp30) cc_final: 0.7306 (tp30) REVERT: J 310 GLN cc_start: 0.8384 (mp10) cc_final: 0.7925 (mp10) REVERT: J 331 ARG cc_start: 0.7098 (ttp-170) cc_final: 0.6817 (ttm-80) REVERT: a 185 MET cc_start: 0.7839 (ptt) cc_final: 0.7529 (ptm) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.2995 time to fit residues: 78.9019 Evaluate side-chains 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 r residue 193 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 Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2507 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= 0.181 Angle : 0.597 10.986 22194 Z= 0.299 Chirality : 0.037 0.239 2688 Planarity : 0.004 0.032 1989 Dihedral : 21.758 178.943 4867 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.53 % Allowed : 20.56 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1239 helix: 1.22 (0.24), residues: 496 sheet: -0.99 (0.44), residues: 155 loop : -0.87 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP r 239 HIS 0.002 0.000 HIS a 12 PHE 0.016 0.001 PHE a 190 TYR 0.014 0.001 TYR q 516 ARG 0.004 0.000 ARG b 130 ********************** 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 183 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 250 ASP cc_start: 0.7383 (t0) cc_final: 0.6938 (t0) REVERT: 7 124 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: A 47 HIS cc_start: 0.6232 (t70) cc_final: 0.5531 (t-90) REVERT: J 247 TYR cc_start: 0.3675 (OUTLIER) cc_final: 0.2503 (m-80) REVERT: J 261 LEU cc_start: 0.4103 (mm) cc_final: 0.3830 (mm) REVERT: J 283 GLU cc_start: 0.6841 (tp30) cc_final: 0.6358 (tp30) REVERT: J 286 ASP cc_start: 0.7671 (m-30) cc_final: 0.7071 (t0) REVERT: J 304 GLU cc_start: 0.8037 (tp30) cc_final: 0.7297 (tp30) REVERT: J 310 GLN cc_start: 0.8366 (mp10) cc_final: 0.7902 (mp10) REVERT: J 331 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6885 (ttm-80) REVERT: a 63 MET cc_start: 0.6506 (tpp) cc_final: 0.6280 (tpt) REVERT: a 120 VAL cc_start: 0.8194 (t) cc_final: 0.7927 (t) REVERT: a 185 MET cc_start: 0.7857 (ptt) cc_final: 0.7578 (ptm) outliers start: 17 outliers final: 12 residues processed: 178 average time/residue: 0.3090 time to fit residues: 79.8058 Evaluate side-chains 176 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 r residue 193 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 J residue 333 THR Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.090482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071773 restraints weight = 52270.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.073078 restraints weight = 29267.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073214 restraints weight = 19279.247| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15677 Z= 0.226 Angle : 0.621 10.858 22194 Z= 0.311 Chirality : 0.038 0.246 2688 Planarity : 0.004 0.032 1989 Dihedral : 21.816 178.914 4867 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.53 % Allowed : 20.92 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1239 helix: 1.15 (0.24), residues: 495 sheet: -1.11 (0.43), residues: 157 loop : -0.93 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP r 239 HIS 0.002 0.001 HIS a 140 PHE 0.018 0.002 PHE r 194 TYR 0.023 0.002 TYR q 227 ARG 0.004 0.000 ARG q 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.29 seconds wall clock time: 52 minutes 48.41 seconds (3168.41 seconds total)