Starting phenix.real_space_refine on Sat Mar 16 07:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/03_2024/7z4k_14500.pdb" } resolution = 3.81 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= 0.001 sd= 0.006 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 134 5.49 5 S 23 5.16 5 C 8405 2.51 5 N 2455 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 11109 Classifications: {'peptide': 1360} Link IDs: {'PTRANS': 35, 'TRANS': 1324} Chain breaks: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1884 Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 75} Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 586 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 21} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 20} Time building chain proxies: 7.71, per 1000 atoms: 0.55 Number of scatterers: 14005 At special positions: 0 Unit cell: (96.2, 124.15, 124.8, 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 23 16.00 P 134 15.00 O 2988 8.00 N 2455 7.00 C 8405 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 - 3.50 Amino acid : False - 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: 6.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 53.9% alpha, 7.9% beta 51 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.661A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.524A pdb=" N LEU B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.571A pdb=" N ILE B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.587A pdb=" N GLN B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.645A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.535A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.741A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.087A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 5.276A pdb=" N GLU B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.020A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.836A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 829 through 833 Processing helix chain 'B' and resid 861 through 865 removed outlier: 4.226A pdb=" N ARG B 864 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 4.959A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 909 through 922 removed outlier: 3.588A pdb=" N LYS B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.892A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.836A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.171A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 removed outlier: 3.651A pdb=" N PHE B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 4.402A pdb=" N LYS B1031 " --> pdb=" O GLN B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1191 through 1195 Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.262A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1317 Processing helix chain 'B' and resid 1341 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 removed outlier: 6.527A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.881A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.514A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.817A pdb=" N LYS B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1052 removed outlier: 4.087A pdb=" N GLU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.720A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 520 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2627 1.33 - 1.45: 4055 1.45 - 1.57: 7554 1.57 - 1.69: 268 1.69 - 1.81: 44 Bond restraints: 14548 Sorted by residual: bond pdb=" O4' DT D -13 " pdb=" C1' DT D -13 " ideal model delta sigma weight residual 1.414 1.378 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C5 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.338 1.364 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C2 DT D -13 " pdb=" O2 DT D -13 " ideal model delta sigma weight residual 1.218 1.242 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" N1 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.380 1.404 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 1.523 1.501 0.022 2.00e-02 2.50e+03 1.18e+00 ... (remaining 14543 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.96: 878 105.96 - 112.96: 8013 112.96 - 119.97: 5033 119.97 - 126.97: 5871 126.97 - 133.97: 426 Bond angle restraints: 20221 Sorted by residual: angle pdb=" N ARG B1333 " pdb=" CA ARG B1333 " pdb=" C ARG B1333 " ideal model delta sigma weight residual 109.07 115.57 -6.50 1.61e+00 3.86e-01 1.63e+01 angle pdb=" N LYS B 918 " pdb=" CA LYS B 918 " pdb=" C LYS B 918 " ideal model delta sigma weight residual 111.28 108.74 2.54 1.09e+00 8.42e-01 5.41e+00 angle pdb=" C4 DT D -12 " pdb=" C5 DT D -12 " pdb=" C7 DT D -12 " ideal model delta sigma weight residual 122.40 119.08 3.32 1.50e+00 4.44e-01 4.89e+00 angle pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " pdb=" C1' DA D 3 " ideal model delta sigma weight residual 101.60 104.75 -3.15 1.50e+00 4.44e-01 4.40e+00 angle pdb=" N LYS B1130 " pdb=" CA LYS B1130 " pdb=" C LYS B1130 " ideal model delta sigma weight residual 114.04 111.55 2.49 1.24e+00 6.50e-01 4.03e+00 ... (remaining 20216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 7837 18.18 - 36.36: 532 36.36 - 54.54: 289 54.54 - 72.71: 147 72.71 - 90.89: 26 Dihedral angle restraints: 8831 sinusoidal: 4834 harmonic: 3997 Sorted by residual: dihedral pdb=" O4' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " pdb=" C2 U A 59 " ideal model delta sinusoidal sigma weight residual -128.00 -62.39 -65.61 1 1.70e+01 3.46e-03 1.95e+01 dihedral pdb=" O5' G A 89 " pdb=" C5' G A 89 " pdb=" C4' G A 89 " pdb=" C3' G A 89 " ideal model delta sinusoidal sigma weight residual 175.00 116.38 58.62 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B1272 " pdb=" CB GLN B1272 " pdb=" CG GLN B1272 " pdb=" CD GLN B1272 " ideal model delta sinusoidal sigma weight residual -60.00 -117.64 57.64 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 8828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1626 0.030 - 0.059: 484 0.059 - 0.089: 124 0.089 - 0.119: 64 0.119 - 0.149: 7 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA VAL B 870 " pdb=" N VAL B 870 " pdb=" C VAL B 870 " pdb=" CB VAL B 870 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" C4' DT D -12 " pdb=" C5' DT D -12 " pdb=" O4' DT D -12 " pdb=" C3' DT D -12 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 448 " pdb=" N ILE B 448 " pdb=" C ILE B 448 " pdb=" CB ILE B 448 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 2302 not shown) Planarity restraints: 2089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ALA B 991 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 992 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 992 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 992 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 992 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 993 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 995 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C THR B 995 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 995 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 996 " 0.012 2.00e-02 2.50e+03 ... (remaining 2086 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 14104 3.28 - 3.82: 25732 3.82 - 4.36: 30178 4.36 - 4.90: 47525 Nonbonded interactions: 118692 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.200 2.440 nonbonded pdb=" OG SER B 512 " pdb=" OE1 GLU B 617 " model vdw 2.222 2.440 nonbonded pdb=" OG SER B1109 " pdb=" OP2 DG C 1 " model vdw 2.235 2.440 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.271 2.440 nonbonded pdb=" N2 G A 33 " pdb=" OP2 A A 36 " model vdw 2.277 2.520 ... (remaining 118687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.940 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: 11.930 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 47.020 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14548 Z= 0.157 Angle : 0.438 6.496 20221 Z= 0.243 Chirality : 0.034 0.149 2305 Planarity : 0.003 0.038 2089 Dihedral : 17.217 90.892 6247 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.99 % Allowed : 4.68 % Favored : 94.33 % 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: 1.12 (0.23), residues: 1356 helix: 1.88 (0.21), residues: 659 sheet: -0.56 (0.49), residues: 118 loop : -0.25 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 464 HIS 0.003 0.000 HIS B 328 PHE 0.006 0.001 PHE B1008 TYR 0.008 0.001 TYR B 882 ARG 0.008 0.000 ARG B1333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 294 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ILE cc_start: 0.7762 (tt) cc_final: 0.7104 (pt) REVERT: B 60 GLU cc_start: 0.9065 (tt0) cc_final: 0.8856 (pp20) REVERT: B 158 LEU cc_start: 0.8742 (mt) cc_final: 0.8407 (mt) REVERT: B 415 HIS cc_start: 0.9023 (m-70) cc_final: 0.8436 (m-70) REVERT: B 433 LEU cc_start: 0.9307 (mt) cc_final: 0.9071 (tt) REVERT: B 504 ASN cc_start: 0.9127 (m-40) cc_final: 0.8817 (p0) REVERT: B 613 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7629 (tp30) REVERT: B 616 LEU cc_start: 0.9683 (mt) cc_final: 0.9440 (mt) REVERT: B 648 MET cc_start: 0.8923 (ttp) cc_final: 0.8474 (ttt) REVERT: B 949 LEU cc_start: 0.7192 (tp) cc_final: 0.6934 (tp) REVERT: B 959 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8183 (pttt) REVERT: B 979 ASN cc_start: 0.8231 (p0) cc_final: 0.7660 (m-40) REVERT: B 1004 LEU cc_start: 0.9017 (mt) cc_final: 0.8761 (mt) REVERT: B 1018 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.6215 (p) REVERT: B 1046 PHE cc_start: 0.7091 (m-10) cc_final: 0.6319 (m-80) REVERT: B 1086 VAL cc_start: 0.8346 (t) cc_final: 0.7771 (t) REVERT: B 1095 VAL cc_start: 0.7857 (t) cc_final: 0.7164 (m) REVERT: B 1169 MET cc_start: 0.8369 (ttp) cc_final: 0.7905 (tmm) REVERT: B 1177 ASN cc_start: 0.9254 (t0) cc_final: 0.8822 (t0) REVERT: B 1180 ASP cc_start: 0.9152 (m-30) cc_final: 0.8789 (m-30) REVERT: B 1190 VAL cc_start: 0.7155 (m) cc_final: 0.6953 (m) outliers start: 12 outliers final: 0 residues processed: 304 average time/residue: 0.3265 time to fit residues: 135.2185 Evaluate side-chains 166 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 134 optimal weight: 8.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN B 99 HIS B 113 HIS B 224 ASN B 228 GLN B 277 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN B 983 HIS ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14548 Z= 0.198 Angle : 0.564 11.698 20221 Z= 0.291 Chirality : 0.036 0.141 2305 Planarity : 0.004 0.042 2089 Dihedral : 20.475 89.625 3361 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.72 % Allowed : 13.30 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.23), residues: 1356 helix: 1.78 (0.20), residues: 662 sheet: -0.62 (0.47), residues: 118 loop : -0.27 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 464 HIS 0.014 0.002 HIS B 930 PHE 0.021 0.001 PHE B1258 TYR 0.024 0.002 TYR B 981 ARG 0.009 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.8777 (mt) cc_final: 0.8570 (mt) REVERT: B 165 ARG cc_start: 0.8321 (ptt180) cc_final: 0.5649 (ptt180) REVERT: B 321 MET cc_start: 0.8486 (mmp) cc_final: 0.7657 (mmp) REVERT: B 433 LEU cc_start: 0.9396 (mt) cc_final: 0.9181 (tt) REVERT: B 504 ASN cc_start: 0.9162 (m-40) cc_final: 0.8933 (p0) REVERT: B 613 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7962 (tp30) REVERT: B 930 HIS cc_start: 0.8532 (m-70) cc_final: 0.8163 (m-70) REVERT: B 979 ASN cc_start: 0.8562 (p0) cc_final: 0.8260 (m110) REVERT: B 1039 TYR cc_start: 0.9188 (m-10) cc_final: 0.8962 (m-10) REVERT: B 1262 HIS cc_start: 0.8186 (m-70) cc_final: 0.7950 (t-90) REVERT: B 1276 PHE cc_start: 0.8317 (t80) cc_final: 0.7734 (t80) REVERT: B 1359 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6685 (mtm110) outliers start: 21 outliers final: 11 residues processed: 178 average time/residue: 0.3139 time to fit residues: 77.8745 Evaluate side-chains 141 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1329 THR Chi-restraints excluded: chain B residue 1359 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 0.0170 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS B 556 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14548 Z= 0.247 Angle : 0.579 7.841 20221 Z= 0.304 Chirality : 0.037 0.216 2305 Planarity : 0.004 0.041 2089 Dihedral : 20.303 88.863 3360 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.12 % Allowed : 14.45 % Favored : 82.43 % 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: 0.74 (0.22), residues: 1356 helix: 1.39 (0.20), residues: 669 sheet: -0.08 (0.54), residues: 87 loop : -0.39 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 464 HIS 0.009 0.002 HIS B 930 PHE 0.018 0.002 PHE B1258 TYR 0.015 0.002 TYR B 451 ARG 0.012 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.8954 (mt) cc_final: 0.8748 (mt) REVERT: B 161 MET cc_start: 0.7965 (tpp) cc_final: 0.7723 (tpp) REVERT: B 165 ARG cc_start: 0.8522 (ptt180) cc_final: 0.5902 (ptt180) REVERT: B 433 LEU cc_start: 0.9453 (mt) cc_final: 0.9170 (tt) REVERT: B 504 ASN cc_start: 0.9167 (m-40) cc_final: 0.8931 (p0) REVERT: B 596 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8755 (m-30) REVERT: B 613 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8146 (tp30) REVERT: B 648 MET cc_start: 0.9349 (tmm) cc_final: 0.8449 (ppp) REVERT: B 879 MET cc_start: 0.3242 (mpp) cc_final: 0.2859 (mpp) REVERT: B 898 ASP cc_start: 0.9600 (m-30) cc_final: 0.9360 (p0) REVERT: B 930 HIS cc_start: 0.8622 (m-70) cc_final: 0.8063 (m-70) REVERT: B 949 LEU cc_start: 0.7430 (tp) cc_final: 0.7171 (pp) REVERT: B 1046 PHE cc_start: 0.7191 (m-80) cc_final: 0.6982 (m-80) REVERT: B 1262 HIS cc_start: 0.8324 (m-70) cc_final: 0.8090 (t-90) REVERT: B 1359 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6748 (mtm110) outliers start: 38 outliers final: 21 residues processed: 161 average time/residue: 0.2806 time to fit residues: 65.5477 Evaluate side-chains 139 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1316 THR Chi-restraints excluded: chain B residue 1359 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN B1252 ASN B1297 HIS B1311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14548 Z= 0.399 Angle : 0.689 8.076 20221 Z= 0.367 Chirality : 0.041 0.221 2305 Planarity : 0.005 0.054 2089 Dihedral : 20.454 90.549 3360 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.53 % Allowed : 16.01 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.21), residues: 1356 helix: 0.61 (0.19), residues: 681 sheet: -0.33 (0.51), residues: 89 loop : -0.66 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 883 HIS 0.009 0.002 HIS B 328 PHE 0.029 0.003 PHE B1276 TYR 0.023 0.002 TYR B 451 ARG 0.010 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: B 161 MET cc_start: 0.8102 (tpp) cc_final: 0.7840 (tpp) REVERT: B 162 ILE cc_start: 0.9092 (pt) cc_final: 0.8890 (pt) REVERT: B 165 ARG cc_start: 0.8453 (ptt180) cc_final: 0.7885 (ptt180) REVERT: B 613 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8264 (tp30) REVERT: B 643 PHE cc_start: 0.6890 (p90) cc_final: 0.6530 (p90) REVERT: B 846 PHE cc_start: 0.9230 (m-80) cc_final: 0.8569 (m-80) REVERT: B 847 LEU cc_start: 0.9207 (tp) cc_final: 0.8947 (mt) REVERT: B 898 ASP cc_start: 0.9657 (m-30) cc_final: 0.9455 (p0) REVERT: B 930 HIS cc_start: 0.8571 (m-70) cc_final: 0.8338 (m-70) REVERT: B 1039 TYR cc_start: 0.9263 (m-10) cc_final: 0.9061 (m-80) REVERT: B 1046 PHE cc_start: 0.7091 (m-80) cc_final: 0.6864 (m-80) REVERT: B 1205 GLU cc_start: 0.8477 (tt0) cc_final: 0.8070 (tp30) REVERT: B 1244 LYS cc_start: 0.7522 (mmtm) cc_final: 0.7203 (pttp) REVERT: B 1359 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6829 (mtm110) outliers start: 43 outliers final: 28 residues processed: 152 average time/residue: 0.2771 time to fit residues: 61.6110 Evaluate side-chains 145 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1329 THR Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1359 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 776 ASN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14548 Z= 0.145 Angle : 0.547 13.737 20221 Z= 0.282 Chirality : 0.036 0.145 2305 Planarity : 0.003 0.036 2089 Dihedral : 20.138 87.917 3360 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 17.57 % Favored : 80.30 % 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: 0.52 (0.22), residues: 1356 helix: 1.22 (0.20), residues: 669 sheet: -0.35 (0.49), residues: 95 loop : -0.48 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 464 HIS 0.007 0.001 HIS B 511 PHE 0.026 0.001 PHE B 290 TYR 0.016 0.002 TYR B 981 ARG 0.007 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 TYR cc_start: 0.8192 (m-80) cc_final: 0.7951 (m-80) REVERT: B 162 ILE cc_start: 0.9067 (pt) cc_final: 0.8790 (pt) REVERT: B 516 GLU cc_start: 0.9457 (mp0) cc_final: 0.9162 (pm20) REVERT: B 626 PHE cc_start: 0.7171 (m-80) cc_final: 0.6565 (m-10) REVERT: B 643 PHE cc_start: 0.6694 (p90) cc_final: 0.5822 (p90) REVERT: B 846 PHE cc_start: 0.9272 (m-80) cc_final: 0.8523 (m-80) REVERT: B 847 LEU cc_start: 0.9175 (tp) cc_final: 0.8898 (mt) REVERT: B 883 TRP cc_start: 0.8558 (m-10) cc_final: 0.8265 (m-10) REVERT: B 930 HIS cc_start: 0.8611 (m-70) cc_final: 0.8333 (m-70) REVERT: B 949 LEU cc_start: 0.7830 (tp) cc_final: 0.7418 (pp) REVERT: B 1039 TYR cc_start: 0.9144 (m-10) cc_final: 0.8922 (m-10) REVERT: B 1046 PHE cc_start: 0.7047 (m-80) cc_final: 0.6838 (m-80) REVERT: B 1182 LEU cc_start: 0.9660 (mt) cc_final: 0.9296 (pp) REVERT: B 1205 GLU cc_start: 0.8462 (tt0) cc_final: 0.7931 (mm-30) REVERT: B 1244 LYS cc_start: 0.7475 (mmtm) cc_final: 0.7083 (pttp) REVERT: B 1359 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6724 (mtm110) outliers start: 26 outliers final: 16 residues processed: 141 average time/residue: 0.2779 time to fit residues: 57.3556 Evaluate side-chains 124 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1359 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14548 Z= 0.352 Angle : 0.671 11.413 20221 Z= 0.352 Chirality : 0.040 0.177 2305 Planarity : 0.004 0.043 2089 Dihedral : 20.325 88.026 3360 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 17.98 % Favored : 79.15 % 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: 0.11 (0.22), residues: 1356 helix: 0.81 (0.20), residues: 676 sheet: -0.58 (0.49), residues: 93 loop : -0.59 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 464 HIS 0.009 0.002 HIS B 328 PHE 0.016 0.002 PHE B1276 TYR 0.026 0.003 TYR B 286 ARG 0.008 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 LEU cc_start: 0.8929 (tp) cc_final: 0.8723 (tt) REVERT: B 499 ASP cc_start: 0.8306 (t70) cc_final: 0.7003 (m-30) REVERT: B 631 MET cc_start: 0.9025 (tpp) cc_final: 0.8750 (tpp) REVERT: B 846 PHE cc_start: 0.9176 (m-80) cc_final: 0.8390 (m-80) REVERT: B 847 LEU cc_start: 0.9249 (tp) cc_final: 0.8971 (mt) REVERT: B 949 LEU cc_start: 0.7914 (tp) cc_final: 0.7426 (pp) REVERT: B 1039 TYR cc_start: 0.9256 (m-10) cc_final: 0.8981 (m-80) REVERT: B 1046 PHE cc_start: 0.7012 (m-80) cc_final: 0.6781 (m-80) REVERT: B 1182 LEU cc_start: 0.9712 (mt) cc_final: 0.9357 (pp) REVERT: B 1205 GLU cc_start: 0.8484 (tt0) cc_final: 0.8165 (pp20) REVERT: B 1244 LYS cc_start: 0.7559 (mmtm) cc_final: 0.7266 (pttp) REVERT: B 1313 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8064 (t80) REVERT: B 1359 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6750 (mtm110) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.2868 time to fit residues: 56.3560 Evaluate side-chains 125 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1359 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14548 Z= 0.219 Angle : 0.606 12.564 20221 Z= 0.312 Chirality : 0.038 0.249 2305 Planarity : 0.005 0.157 2089 Dihedral : 20.246 86.364 3360 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.87 % Allowed : 19.29 % Favored : 77.83 % 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: 0.29 (0.22), residues: 1356 helix: 1.03 (0.20), residues: 668 sheet: -0.67 (0.51), residues: 93 loop : -0.54 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 464 HIS 0.008 0.001 HIS B1264 PHE 0.027 0.001 PHE B 518 TYR 0.020 0.002 TYR B 823 ARG 0.018 0.001 ARG B1212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.8299 (t70) cc_final: 0.7010 (m-30) REVERT: B 626 PHE cc_start: 0.7351 (m-80) cc_final: 0.6687 (m-80) REVERT: B 763 MET cc_start: 0.6879 (mmm) cc_final: 0.6526 (mmm) REVERT: B 846 PHE cc_start: 0.9160 (m-80) cc_final: 0.8342 (m-80) REVERT: B 847 LEU cc_start: 0.9227 (tp) cc_final: 0.8925 (mt) REVERT: B 949 LEU cc_start: 0.7838 (tp) cc_final: 0.7430 (pp) REVERT: B 1039 TYR cc_start: 0.9226 (m-10) cc_final: 0.8890 (m-80) REVERT: B 1046 PHE cc_start: 0.7087 (m-80) cc_final: 0.6873 (m-80) REVERT: B 1205 GLU cc_start: 0.8418 (tt0) cc_final: 0.8013 (pp20) REVERT: B 1244 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7226 (pttp) REVERT: B 1261 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6815 (pp30) REVERT: B 1313 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7950 (t80) outliers start: 35 outliers final: 24 residues processed: 133 average time/residue: 0.2814 time to fit residues: 55.1121 Evaluate side-chains 125 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1313 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 844 GLN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14548 Z= 0.316 Angle : 0.661 12.727 20221 Z= 0.344 Chirality : 0.039 0.223 2305 Planarity : 0.005 0.098 2089 Dihedral : 20.344 87.435 3360 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.71 % Allowed : 19.62 % Favored : 77.67 % 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: 0.00 (0.22), residues: 1356 helix: 0.81 (0.19), residues: 667 sheet: -0.89 (0.50), residues: 98 loop : -0.70 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 464 HIS 0.015 0.002 HIS B 930 PHE 0.023 0.002 PHE B 518 TYR 0.038 0.003 TYR B1265 ARG 0.008 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.8442 (t70) cc_final: 0.7086 (m-30) REVERT: B 626 PHE cc_start: 0.7370 (m-80) cc_final: 0.7082 (m-10) REVERT: B 847 LEU cc_start: 0.9229 (tp) cc_final: 0.8967 (mt) REVERT: B 890 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9337 (pttp) REVERT: B 930 HIS cc_start: 0.8606 (m-70) cc_final: 0.8318 (m90) REVERT: B 949 LEU cc_start: 0.7909 (tp) cc_final: 0.7451 (pp) REVERT: B 1169 MET cc_start: 0.8407 (mmm) cc_final: 0.8173 (mmm) REVERT: B 1205 GLU cc_start: 0.8533 (tt0) cc_final: 0.8103 (pp20) REVERT: B 1244 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7350 (pttp) REVERT: B 1313 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8006 (t80) outliers start: 33 outliers final: 26 residues processed: 121 average time/residue: 0.2405 time to fit residues: 44.3144 Evaluate side-chains 121 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1313 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14548 Z= 0.316 Angle : 0.666 12.336 20221 Z= 0.348 Chirality : 0.041 0.317 2305 Planarity : 0.005 0.067 2089 Dihedral : 20.414 86.779 3360 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.87 % Allowed : 19.79 % Favored : 77.34 % 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 (0.22), residues: 1356 helix: 0.75 (0.20), residues: 660 sheet: -0.91 (0.51), residues: 94 loop : -0.73 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 464 HIS 0.017 0.002 HIS B 930 PHE 0.036 0.002 PHE B 518 TYR 0.027 0.002 TYR B1265 ARG 0.007 0.001 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.8476 (t70) cc_final: 0.7155 (m-30) REVERT: B 648 MET cc_start: 0.9575 (tmm) cc_final: 0.9230 (ppp) REVERT: B 682 PHE cc_start: 0.9184 (m-80) cc_final: 0.8711 (m-10) REVERT: B 763 MET cc_start: 0.7032 (mmm) cc_final: 0.6644 (mmm) REVERT: B 847 LEU cc_start: 0.9212 (tp) cc_final: 0.8945 (mt) REVERT: B 930 HIS cc_start: 0.8628 (m-70) cc_final: 0.8340 (m90) REVERT: B 949 LEU cc_start: 0.7933 (tp) cc_final: 0.7489 (pp) REVERT: B 1205 GLU cc_start: 0.8511 (tt0) cc_final: 0.8069 (tp30) REVERT: B 1244 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7390 (pttp) REVERT: B 1313 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8013 (t80) outliers start: 35 outliers final: 27 residues processed: 124 average time/residue: 0.2447 time to fit residues: 46.6144 Evaluate side-chains 123 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1313 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 40.0000 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14548 Z= 0.224 Angle : 0.611 12.834 20221 Z= 0.316 Chirality : 0.038 0.297 2305 Planarity : 0.004 0.060 2089 Dihedral : 20.312 86.570 3360 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.38 % Allowed : 20.44 % Favored : 77.18 % 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: 0.09 (0.22), residues: 1356 helix: 0.88 (0.20), residues: 667 sheet: -0.93 (0.50), residues: 94 loop : -0.63 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 464 HIS 0.016 0.002 HIS B 930 PHE 0.034 0.002 PHE B 518 TYR 0.026 0.002 TYR B 812 ARG 0.007 0.001 ARG B 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.8508 (t70) cc_final: 0.7232 (m-30) REVERT: B 648 MET cc_start: 0.9580 (tmm) cc_final: 0.9164 (ppp) REVERT: B 682 PHE cc_start: 0.9148 (m-80) cc_final: 0.8704 (m-10) REVERT: B 763 MET cc_start: 0.7013 (mmm) cc_final: 0.6629 (mmm) REVERT: B 847 LEU cc_start: 0.9242 (tp) cc_final: 0.8969 (mt) REVERT: B 930 HIS cc_start: 0.8627 (m-70) cc_final: 0.8335 (m90) REVERT: B 949 LEU cc_start: 0.7878 (tp) cc_final: 0.7480 (pp) REVERT: B 1105 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: B 1244 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7310 (pttp) REVERT: B 1313 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7914 (t80) outliers start: 29 outliers final: 25 residues processed: 116 average time/residue: 0.2517 time to fit residues: 44.6008 Evaluate side-chains 121 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1105 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1313 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 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 = 0.3747 r_free = 0.3747 target = 0.072230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052409 restraints weight = 92370.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.053873 restraints weight = 54806.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054705 restraints weight = 39608.776| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14548 Z= 0.264 Angle : 0.624 12.636 20221 Z= 0.325 Chirality : 0.039 0.285 2305 Planarity : 0.004 0.065 2089 Dihedral : 20.314 87.378 3360 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.55 % Allowed : 20.53 % Favored : 76.93 % 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: -0.01 (0.22), residues: 1356 helix: 0.78 (0.19), residues: 675 sheet: -0.88 (0.50), residues: 94 loop : -0.70 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 464 HIS 0.016 0.002 HIS B 930 PHE 0.035 0.002 PHE B 518 TYR 0.027 0.002 TYR B 812 ARG 0.009 0.001 ARG B 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.44 seconds wall clock time: 51 minutes 35.75 seconds (3095.75 seconds total)