Starting phenix.real_space_refine on Sun Dec 10 09:04:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/12_2023/7z4k_14500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/12_2023/7z4k_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_14500/12_2023/7z4k_14500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/12_2023/7z4k_14500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/12_2023/7z4k_14500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4k_14500/12_2023/7z4k_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-1.21rc1-5172/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: 8.34, per 1000 atoms: 0.60 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: 6.71 Conformation dependent library (CDL) restraints added in 2.4 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: 6.07 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: 7.40 Time building geometry restraints manager: 7.10 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: 7811 18.18 - 36.36: 510 36.36 - 54.54: 272 54.54 - 72.71: 124 72.71 - 90.89: 26 Dihedral angle restraints: 8743 sinusoidal: 4746 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 8740 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.180 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 48.520 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.340 ------------------------------------------------------------------------------- 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 : 16.736 90.892 6159 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 : 1.399 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 outliers start: 12 outliers final: 0 residues processed: 304 average time/residue: 0.3369 time to fit residues: 139.8785 Evaluate side-chains 162 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 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: 0.7687 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14548 Z= 0.205 Angle : 0.573 12.252 20221 Z= 0.296 Chirality : 0.036 0.154 2305 Planarity : 0.004 0.041 2089 Dihedral : 19.824 89.511 3272 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.89 % Allowed : 13.14 % 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: 0.94 (0.22), residues: 1356 helix: 1.68 (0.20), residues: 663 sheet: -0.28 (0.54), residues: 86 loop : -0.39 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 464 HIS 0.013 0.002 HIS B 930 PHE 0.022 0.001 PHE B1258 TYR 0.025 0.002 TYR B1001 ARG 0.008 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 185 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.373 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 outliers start: 23 outliers final: 11 residues processed: 180 average time/residue: 0.3165 time to fit residues: 79.5419 Evaluate side-chains 135 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1212 time to fit residues: 4.2667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 ASN B1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14548 Z= 0.374 Angle : 0.670 8.223 20221 Z= 0.356 Chirality : 0.040 0.181 2305 Planarity : 0.005 0.048 2089 Dihedral : 19.879 90.176 3272 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.55 % Allowed : 15.60 % Favored : 81.86 % 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: 0.33 (0.22), residues: 1356 helix: 1.04 (0.19), residues: 672 sheet: -0.35 (0.50), residues: 99 loop : -0.57 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 464 HIS 0.019 0.003 HIS B 930 PHE 0.020 0.002 PHE B 518 TYR 0.021 0.002 TYR B 451 ARG 0.009 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 156 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.493 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 outliers start: 31 outliers final: 16 residues processed: 147 average time/residue: 0.3129 time to fit residues: 66.0646 Evaluate side-chains 123 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1366 time to fit residues: 5.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14548 Z= 0.274 Angle : 0.606 10.536 20221 Z= 0.320 Chirality : 0.038 0.239 2305 Planarity : 0.004 0.046 2089 Dihedral : 19.777 89.813 3272 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.89 % Allowed : 17.16 % Favored : 80.95 % 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: 0.27 (0.22), residues: 1356 helix: 0.97 (0.20), residues: 675 sheet: -0.46 (0.47), residues: 99 loop : -0.56 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 464 HIS 0.013 0.002 HIS B1262 PHE 0.019 0.002 PHE B1276 TYR 0.013 0.002 TYR B 451 ARG 0.007 0.001 ARG B 884 *********************** 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 145 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 137 average time/residue: 0.2727 time to fit residues: 55.7676 Evaluate side-chains 115 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1416 time to fit residues: 4.5191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 869 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: 0.7836 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14548 Z= 0.160 Angle : 0.549 13.237 20221 Z= 0.286 Chirality : 0.036 0.181 2305 Planarity : 0.003 0.037 2089 Dihedral : 19.560 89.067 3272 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.89 % Allowed : 16.91 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.22), residues: 1356 helix: 1.30 (0.20), residues: 673 sheet: -0.67 (0.47), residues: 103 loop : -0.47 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 464 HIS 0.019 0.002 HIS B 930 PHE 0.023 0.001 PHE B 290 TYR 0.018 0.001 TYR B1265 ARG 0.008 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 149 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.382 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 outliers start: 23 outliers final: 10 residues processed: 138 average time/residue: 0.2680 time to fit residues: 56.3672 Evaluate side-chains 121 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1313 time to fit residues: 4.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 556 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14548 Z= 0.291 Angle : 0.613 11.270 20221 Z= 0.322 Chirality : 0.038 0.177 2305 Planarity : 0.004 0.042 2089 Dihedral : 19.635 87.685 3272 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.31 % Allowed : 18.23 % 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: 0.32 (0.22), residues: 1356 helix: 1.10 (0.20), residues: 676 sheet: -0.75 (0.49), residues: 93 loop : -0.60 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 464 HIS 0.010 0.002 HIS B 930 PHE 0.020 0.002 PHE B 290 TYR 0.022 0.003 TYR B1039 ARG 0.010 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 125 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.468 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 outliers start: 16 outliers final: 7 residues processed: 122 average time/residue: 0.2776 time to fit residues: 50.5390 Evaluate side-chains 100 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1294 time to fit residues: 3.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 81 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 844 GLN ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 14548 Z= 0.418 Angle : 0.754 10.949 20221 Z= 0.397 Chirality : 0.043 0.200 2305 Planarity : 0.005 0.050 2089 Dihedral : 19.945 87.309 3272 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.97 % Allowed : 19.62 % Favored : 78.41 % 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: -0.51 (0.21), residues: 1356 helix: 0.38 (0.19), residues: 673 sheet: -1.07 (0.50), residues: 99 loop : -0.96 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 464 HIS 0.019 0.003 HIS B 930 PHE 0.031 0.003 PHE B 518 TYR 0.038 0.003 TYR B1036 ARG 0.008 0.001 ARG B 115 *********************** 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 121 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 115 average time/residue: 0.2669 time to fit residues: 46.5746 Evaluate side-chains 101 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1317 time to fit residues: 4.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14548 Z= 0.227 Angle : 0.631 12.660 20221 Z= 0.325 Chirality : 0.039 0.366 2305 Planarity : 0.004 0.049 2089 Dihedral : 19.715 86.035 3272 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.82 % Allowed : 20.11 % Favored : 79.06 % 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 (0.22), residues: 1356 helix: 0.82 (0.20), residues: 677 sheet: -0.92 (0.51), residues: 99 loop : -0.77 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 464 HIS 0.008 0.002 HIS B 930 PHE 0.020 0.002 PHE B 290 TYR 0.020 0.002 TYR B 812 ARG 0.011 0.000 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 110 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.2528 time to fit residues: 40.7773 Evaluate side-chains 97 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2162 time to fit residues: 4.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.0030 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- 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** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14548 Z= 0.325 Angle : 0.677 12.800 20221 Z= 0.351 Chirality : 0.041 0.325 2305 Planarity : 0.005 0.070 2089 Dihedral : 19.805 87.441 3272 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.57 % Allowed : 21.02 % Favored : 78.41 % 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: -0.21 (0.22), residues: 1356 helix: 0.72 (0.20), residues: 665 sheet: -1.06 (0.50), residues: 99 loop : -0.90 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 18 HIS 0.019 0.002 HIS B 930 PHE 0.018 0.002 PHE B 966 TYR 0.024 0.002 TYR B 812 ARG 0.009 0.001 ARG B 220 *********************** 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 102 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 100 average time/residue: 0.2816 time to fit residues: 42.4096 Evaluate side-chains 87 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14548 Z= 0.252 Angle : 0.659 14.799 20221 Z= 0.342 Chirality : 0.040 0.303 2305 Planarity : 0.004 0.054 2089 Dihedral : 19.741 86.527 3272 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.41 % Allowed : 22.09 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.22), residues: 1356 helix: 0.75 (0.20), residues: 672 sheet: -1.12 (0.49), residues: 99 loop : -0.81 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 18 HIS 0.008 0.002 HIS B 930 PHE 0.042 0.002 PHE B 626 TYR 0.025 0.002 TYR B 812 ARG 0.012 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 98 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.2551 time to fit residues: 38.4463 Evaluate side-chains 92 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1507 time to fit residues: 2.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 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 776 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 = 0.3766 r_free = 0.3766 target = 0.072655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052871 restraints weight = 91028.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054349 restraints weight = 54308.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055256 restraints weight = 39105.399| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14548 Z= 0.267 Angle : 0.666 14.918 20221 Z= 0.342 Chirality : 0.040 0.293 2305 Planarity : 0.004 0.054 2089 Dihedral : 19.721 87.277 3272 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.33 % Allowed : 21.92 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1356 helix: 0.75 (0.20), residues: 672 sheet: -1.13 (0.50), residues: 99 loop : -0.83 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 18 HIS 0.007 0.002 HIS B 930 PHE 0.047 0.002 PHE B 626 TYR 0.027 0.002 TYR B 812 ARG 0.012 0.001 ARG B 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.59 seconds wall clock time: 50 minutes 31.78 seconds (3031.78 seconds total)