Starting phenix.real_space_refine on Sat Feb 17 06:29:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/02_2024/7z4e_14494.pdb" } resolution = 4.14 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= 0.003 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3728 atoms to isotropic. 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 138 5.49 5 S 23 5.16 5 C 8436 2.51 5 N 2467 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14069 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 11089 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 35, 'TRANS': 1321} 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': 8, 'rna3p_pur': 46, 'rna3p_pyr': 28} Link IDs: {'rna2p': 14, 'rna3p': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Inner-chain residues flagged as termini: ['pdbres=" DT D -3 "'] Classifications: {'DNA': 25} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 24} Time building chain proxies: 7.60, per 1000 atoms: 0.54 Number of scatterers: 14069 At special positions: 0 Unit cell: (94.9, 131.95, 122.2, 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 138 15.00 O 3005 8.00 N 2467 7.00 C 8436 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: 6.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 53.6% alpha, 8.0% beta 50 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.121A pdb=" N ARG B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) 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: 3.737A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.737A pdb=" N PHE B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.727A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (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: 4.097A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.269A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.525A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.686A 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 removed outlier: 3.604A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) 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 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.450A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 removed outlier: 3.769A pdb=" N HIS B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) 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 832 through 836 Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.577A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.950A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.950A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.345A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1152 through 1155 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 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1281 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 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.519A pdb=" N ILE B 43 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 45 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 30 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.541A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.604A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050 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 1107 through 1111 removed outlier: 6.668A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1157 through 1167 removed outlier: 3.516A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B1166 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 517 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 4323 1.35 - 1.50: 4657 1.50 - 1.65: 5599 1.65 - 1.80: 29 1.80 - 1.95: 15 Bond restraints: 14623 Sorted by residual: bond pdb=" SD MET B1021 " pdb=" CE MET B1021 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.10e+01 bond pdb=" CG MET B1021 " pdb=" SD MET B1021 " ideal model delta sigma weight residual 1.803 1.950 -0.147 2.50e-02 1.60e+03 3.46e+01 bond pdb=" O3' G A 43 " pdb=" P U A 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.51e+00 bond pdb=" N LYS B 163 " pdb=" CA LYS B 163 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.54e+00 bond pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.69e+00 ... (remaining 14618 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.86: 879 105.86 - 112.88: 8028 112.88 - 119.90: 4934 119.90 - 126.91: 6053 126.91 - 133.93: 447 Bond angle restraints: 20341 Sorted by residual: angle pdb=" N GLU B 627 " pdb=" CA GLU B 627 " pdb=" C GLU B 627 " ideal model delta sigma weight residual 114.75 107.53 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" C ARG B 403 " pdb=" CA ARG B 403 " pdb=" CB ARG B 403 " ideal model delta sigma weight residual 109.53 116.08 -6.55 1.65e+00 3.67e-01 1.58e+01 angle pdb=" N GLN B 402 " pdb=" CA GLN B 402 " pdb=" C GLN B 402 " ideal model delta sigma weight residual 111.14 107.16 3.98 1.08e+00 8.57e-01 1.36e+01 angle pdb=" N ARG B 100 " pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 110.97 107.40 3.57 1.09e+00 8.42e-01 1.08e+01 angle pdb=" CA LEU B1206 " pdb=" C LEU B1206 " pdb=" N GLU B1207 " ideal model delta sigma weight residual 115.75 120.02 -4.27 1.34e+00 5.57e-01 1.02e+01 ... (remaining 20336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 7925 21.26 - 42.52: 548 42.52 - 63.78: 350 63.78 - 85.04: 45 85.04 - 106.30: 6 Dihedral angle restraints: 8874 sinusoidal: 4884 harmonic: 3990 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 -66.06 -61.94 1 1.70e+01 3.46e-03 1.76e+01 dihedral pdb=" O4' G A 33 " pdb=" C1' G A 33 " pdb=" N9 G A 33 " pdb=" C4 G A 33 " ideal model delta sinusoidal sigma weight residual 70.00 -2.44 72.44 1 2.00e+01 2.50e-03 1.68e+01 dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual -90.00 -33.97 -56.03 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 8871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1783 0.039 - 0.077: 411 0.077 - 0.116: 109 0.116 - 0.155: 12 0.155 - 0.194: 4 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C1' U A 23 " pdb=" O4' U A 23 " pdb=" C2' U A 23 " pdb=" N1 U A 23 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C1' U A 66 " pdb=" O4' U A 66 " pdb=" C2' U A 66 " pdb=" N1 U A 66 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C3' C A 20 " pdb=" C4' C A 20 " pdb=" O3' C A 20 " pdb=" C2' C A 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2316 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 21 " -0.009 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G A 21 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 21 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G A 21 " 0.018 2.00e-02 2.50e+03 pdb=" C5 G A 21 " -0.008 2.00e-02 2.50e+03 pdb=" C6 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 21 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A 21 " 0.030 2.00e-02 2.50e+03 pdb=" N3 G A 21 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G A 21 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 20 " -0.024 2.00e-02 2.50e+03 1.47e-02 4.85e+00 pdb=" N1 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" O2 C A 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C A 20 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C A 20 " -0.028 2.00e-02 2.50e+03 pdb=" C5 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 20 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 24 " -0.023 2.00e-02 2.50e+03 1.30e-02 3.83e+00 pdb=" N1 U A 24 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U A 24 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U A 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 24 " 0.003 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 13990 3.28 - 3.82: 25029 3.82 - 4.36: 29663 4.36 - 4.90: 45961 Nonbonded interactions: 115721 Sorted by model distance: nonbonded pdb=" O2' U A 59 " pdb=" OP1 C A 60 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP B1267 " pdb=" OH TYR B1294 " model vdw 2.217 2.440 nonbonded pdb=" O ALA B1227 " pdb=" N2 G A 89 " model vdw 2.241 2.520 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.243 2.520 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.252 2.440 ... (remaining 115716 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: 0.010 Normalize map: mean=0, sd=1: 17.200 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: 0.000 Extract box with map and model: 10.960 Check model and map are aligned: 0.180 Set scattering table: 0.150 Process input model: 45.050 Find NCS groups from input model: 0.470 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.004 0.160 14623 Z= 0.224 Angle : 0.547 7.220 20341 Z= 0.329 Chirality : 0.037 0.194 2319 Planarity : 0.003 0.044 2088 Dihedral : 17.904 106.299 6294 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.64 % Allowed : 5.02 % Favored : 93.34 % 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: 0.67 (0.23), residues: 1353 helix: 1.29 (0.21), residues: 667 sheet: -0.28 (0.50), residues: 111 loop : -0.33 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 PHE 0.006 0.001 PHE B 97 TYR 0.007 0.001 TYR B1141 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.476 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: B 77 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8126 (t0) REVERT: B 139 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8377 (mtp180) REVERT: B 161 MET cc_start: 0.8380 (mtt) cc_final: 0.8030 (mtt) REVERT: B 415 HIS cc_start: 0.8890 (m90) cc_final: 0.8608 (m-70) REVERT: B 419 LEU cc_start: 0.9571 (tt) cc_final: 0.9324 (pp) REVERT: B 534 MET cc_start: 0.4961 (mtp) cc_final: 0.3639 (ttp) REVERT: B 659 TRP cc_start: 0.7501 (m100) cc_final: 0.6816 (m100) REVERT: B 822 MET cc_start: 0.9514 (tpt) cc_final: 0.9082 (tpp) REVERT: B 848 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4143 (mptt) REVERT: B 856 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.8812 (t) REVERT: B 933 GLN cc_start: 0.9606 (tm-30) cc_final: 0.9222 (pm20) REVERT: B 958 LEU cc_start: 0.9125 (mt) cc_final: 0.8607 (mt) REVERT: B 966 PHE cc_start: 0.9123 (t80) cc_final: 0.8685 (t80) REVERT: B 1213 MET cc_start: 0.7729 (mtm) cc_final: 0.6900 (ttm) REVERT: B 1219 GLU cc_start: 0.8722 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 1355 LEU cc_start: 0.8630 (mt) cc_final: 0.8319 (mt) outliers start: 20 outliers final: 5 residues processed: 213 average time/residue: 0.3302 time to fit residues: 96.6385 Evaluate side-chains 107 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 0.0030 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 341 GLN B 412 HIS B 726 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14623 Z= 0.188 Angle : 0.510 8.231 20341 Z= 0.275 Chirality : 0.035 0.154 2319 Planarity : 0.004 0.053 2088 Dihedral : 20.779 107.191 3411 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.08 % Allowed : 1.73 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.23), residues: 1353 helix: 1.63 (0.20), residues: 682 sheet: 0.15 (0.54), residues: 87 loop : -0.08 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.005 0.001 HIS B1262 PHE 0.016 0.001 PHE B1313 TYR 0.012 0.001 TYR B1016 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.437 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: B 415 HIS cc_start: 0.8941 (m90) cc_final: 0.8335 (m-70) REVERT: B 534 MET cc_start: 0.6006 (mtp) cc_final: 0.4818 (ptp) REVERT: B 659 TRP cc_start: 0.7614 (m100) cc_final: 0.7132 (m100) REVERT: B 718 ASP cc_start: 0.9309 (m-30) cc_final: 0.8757 (p0) REVERT: B 781 MET cc_start: 0.8849 (mmm) cc_final: 0.8623 (mmm) REVERT: B 822 MET cc_start: 0.9540 (tpt) cc_final: 0.9221 (tpp) REVERT: B 933 GLN cc_start: 0.9595 (tm-30) cc_final: 0.9220 (pm20) REVERT: B 1094 ILE cc_start: 0.8401 (mm) cc_final: 0.8131 (tp) REVERT: B 1095 VAL cc_start: 0.9543 (t) cc_final: 0.9152 (p) REVERT: B 1213 MET cc_start: 0.7746 (mtm) cc_final: 0.7030 (ttm) REVERT: B 1219 GLU cc_start: 0.8773 (tt0) cc_final: 0.8412 (tm-30) REVERT: B 1350 GLN cc_start: 0.9025 (mt0) cc_final: 0.8773 (mm-40) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2749 time to fit residues: 48.8285 Evaluate side-chains 80 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 45 optimal weight: 0.0770 chunk 107 optimal weight: 10.0000 overall best weight: 4.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN B 415 HIS ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14623 Z= 0.264 Angle : 0.567 7.909 20341 Z= 0.305 Chirality : 0.036 0.147 2319 Planarity : 0.004 0.047 2088 Dihedral : 21.140 107.401 3411 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.53 % 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: 1.16 (0.23), residues: 1353 helix: 1.68 (0.20), residues: 674 sheet: 0.17 (0.56), residues: 82 loop : -0.14 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 464 HIS 0.006 0.001 HIS B1262 PHE 0.013 0.002 PHE B 97 TYR 0.022 0.002 TYR B 136 ARG 0.014 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.424 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 321 MET cc_start: 0.9023 (tpp) cc_final: 0.8817 (tpp) REVERT: B 383 MET cc_start: 0.8522 (mmp) cc_final: 0.7955 (mmm) REVERT: B 534 MET cc_start: 0.6313 (mtp) cc_final: 0.5246 (ptp) REVERT: B 718 ASP cc_start: 0.9343 (m-30) cc_final: 0.8852 (p0) REVERT: B 740 THR cc_start: 0.8968 (m) cc_final: 0.8751 (m) REVERT: B 781 MET cc_start: 0.9114 (mmm) cc_final: 0.8884 (mmm) REVERT: B 794 GLN cc_start: 0.9632 (mm-40) cc_final: 0.9375 (mm-40) REVERT: B 798 GLU cc_start: 0.9335 (tp30) cc_final: 0.9128 (pt0) REVERT: B 822 MET cc_start: 0.9550 (tpt) cc_final: 0.8669 (tpp) REVERT: B 823 TYR cc_start: 0.7924 (m-10) cc_final: 0.7582 (m-10) REVERT: B 929 LYS cc_start: 0.9639 (mtmm) cc_final: 0.9401 (mttt) REVERT: B 933 GLN cc_start: 0.9574 (tm-30) cc_final: 0.9290 (pt0) REVERT: B 1219 GLU cc_start: 0.8862 (tt0) cc_final: 0.8287 (tm-30) REVERT: B 1242 TYR cc_start: 0.7902 (t80) cc_final: 0.7516 (t80) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.2635 time to fit residues: 40.0080 Evaluate side-chains 72 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14623 Z= 0.295 Angle : 0.584 8.448 20341 Z= 0.317 Chirality : 0.037 0.154 2319 Planarity : 0.004 0.048 2088 Dihedral : 21.293 107.591 3411 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.89 (0.23), residues: 1353 helix: 1.44 (0.20), residues: 684 sheet: -0.23 (0.61), residues: 69 loop : -0.21 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 464 HIS 0.006 0.002 HIS B1262 PHE 0.016 0.002 PHE B 966 TYR 0.016 0.002 TYR B 136 ARG 0.012 0.001 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.537 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 383 MET cc_start: 0.8434 (mmp) cc_final: 0.7900 (mmm) REVERT: B 450 TYR cc_start: 0.6799 (m-80) cc_final: 0.6539 (m-10) REVERT: B 534 MET cc_start: 0.6130 (mtp) cc_final: 0.5133 (ptp) REVERT: B 718 ASP cc_start: 0.9309 (m-30) cc_final: 0.8838 (p0) REVERT: B 781 MET cc_start: 0.9195 (mmm) cc_final: 0.8905 (mmm) REVERT: B 798 GLU cc_start: 0.9372 (tp30) cc_final: 0.9163 (pt0) REVERT: B 929 LYS cc_start: 0.9652 (mtmm) cc_final: 0.9351 (mttt) REVERT: B 933 GLN cc_start: 0.9579 (tm-30) cc_final: 0.9210 (pm20) REVERT: B 1213 MET cc_start: 0.7503 (mmm) cc_final: 0.7013 (tpp) REVERT: B 1219 GLU cc_start: 0.8898 (tt0) cc_final: 0.8208 (tm-30) REVERT: B 1242 TYR cc_start: 0.8055 (t80) cc_final: 0.7688 (t80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2328 time to fit residues: 33.7263 Evaluate side-chains 71 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 127 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 overall best weight: 4.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 808 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14623 Z= 0.235 Angle : 0.524 7.349 20341 Z= 0.286 Chirality : 0.036 0.148 2319 Planarity : 0.003 0.045 2088 Dihedral : 21.166 106.092 3411 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.08 % Allowed : 1.81 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.23), residues: 1353 helix: 1.64 (0.20), residues: 683 sheet: -0.44 (0.60), residues: 74 loop : -0.15 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 464 HIS 0.005 0.001 HIS B 328 PHE 0.014 0.002 PHE B 970 TYR 0.020 0.002 TYR B1265 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.548 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: 0.9287 (mpp) cc_final: 0.8452 (ttt) REVERT: B 383 MET cc_start: 0.8365 (mmp) cc_final: 0.7857 (mmm) REVERT: B 450 TYR cc_start: 0.6866 (m-80) cc_final: 0.6582 (m-10) REVERT: B 534 MET cc_start: 0.6067 (mtp) cc_final: 0.5263 (ptm) REVERT: B 659 TRP cc_start: 0.8176 (m100) cc_final: 0.7732 (m100) REVERT: B 718 ASP cc_start: 0.9333 (m-30) cc_final: 0.8857 (p0) REVERT: B 781 MET cc_start: 0.9238 (mmm) cc_final: 0.8991 (mmm) REVERT: B 822 MET cc_start: 0.9447 (mmp) cc_final: 0.8822 (mmm) REVERT: B 929 LYS cc_start: 0.9649 (mtmm) cc_final: 0.9325 (mttt) REVERT: B 933 GLN cc_start: 0.9553 (tm-30) cc_final: 0.9118 (pm20) REVERT: B 1213 MET cc_start: 0.7449 (mmm) cc_final: 0.7124 (tpp) REVERT: B 1219 GLU cc_start: 0.8873 (tt0) cc_final: 0.8203 (tm-30) REVERT: B 1242 TYR cc_start: 0.7994 (t80) cc_final: 0.7635 (t80) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2353 time to fit residues: 34.1829 Evaluate side-chains 69 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 83 optimal weight: 40.0000 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN B 920 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14623 Z= 0.354 Angle : 0.639 10.360 20341 Z= 0.346 Chirality : 0.039 0.185 2319 Planarity : 0.004 0.052 2088 Dihedral : 21.580 108.407 3411 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.64 (0.23), residues: 1353 helix: 1.21 (0.20), residues: 683 sheet: -0.56 (0.57), residues: 80 loop : -0.26 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 464 HIS 0.006 0.002 HIS B1262 PHE 0.017 0.002 PHE B 53 TYR 0.023 0.002 TYR B 128 ARG 0.010 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.505 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 90 MET cc_start: 0.9320 (mpp) cc_final: 0.8922 (mpp) REVERT: B 383 MET cc_start: 0.8264 (mmp) cc_final: 0.7871 (mmm) REVERT: B 534 MET cc_start: 0.6131 (mtp) cc_final: 0.5156 (ttp) REVERT: B 659 TRP cc_start: 0.8312 (m100) cc_final: 0.7896 (m100) REVERT: B 718 ASP cc_start: 0.9418 (m-30) cc_final: 0.8962 (p0) REVERT: B 781 MET cc_start: 0.9220 (mmm) cc_final: 0.8939 (mmm) REVERT: B 822 MET cc_start: 0.9327 (mmp) cc_final: 0.8614 (mmm) REVERT: B 823 TYR cc_start: 0.8520 (m-10) cc_final: 0.8296 (m-10) REVERT: B 934 ILE cc_start: 0.9791 (pt) cc_final: 0.9570 (pt) REVERT: B 1167 THR cc_start: 0.9375 (p) cc_final: 0.8923 (p) REVERT: B 1170 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8601 (mp0) REVERT: B 1213 MET cc_start: 0.7521 (mmm) cc_final: 0.7297 (tpp) REVERT: B 1219 GLU cc_start: 0.8866 (tt0) cc_final: 0.8458 (tt0) REVERT: B 1242 TYR cc_start: 0.8217 (t80) cc_final: 0.7878 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2614 time to fit residues: 32.5810 Evaluate side-chains 62 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14623 Z= 0.199 Angle : 0.509 7.403 20341 Z= 0.277 Chirality : 0.035 0.160 2319 Planarity : 0.004 0.066 2088 Dihedral : 21.203 105.525 3411 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 1.00 (0.23), residues: 1353 helix: 1.57 (0.20), residues: 689 sheet: -0.07 (0.63), residues: 67 loop : -0.26 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 464 HIS 0.005 0.001 HIS B 160 PHE 0.011 0.001 PHE B 970 TYR 0.014 0.001 TYR B1265 ARG 0.005 0.000 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.534 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: B 383 MET cc_start: 0.8381 (mmp) cc_final: 0.7942 (mmm) REVERT: B 450 TYR cc_start: 0.6923 (m-80) cc_final: 0.6577 (m-10) REVERT: B 534 MET cc_start: 0.6012 (mtp) cc_final: 0.5363 (ptm) REVERT: B 659 TRP cc_start: 0.8308 (m100) cc_final: 0.7798 (m100) REVERT: B 718 ASP cc_start: 0.9412 (m-30) cc_final: 0.8948 (p0) REVERT: B 781 MET cc_start: 0.9237 (mmm) cc_final: 0.8963 (mmm) REVERT: B 822 MET cc_start: 0.9380 (mmp) cc_final: 0.8770 (mmm) REVERT: B 1169 MET cc_start: 0.8828 (mmt) cc_final: 0.8517 (mmt) REVERT: B 1213 MET cc_start: 0.7430 (mmm) cc_final: 0.7141 (tpp) REVERT: B 1219 GLU cc_start: 0.8806 (tt0) cc_final: 0.8461 (tt0) REVERT: B 1242 TYR cc_start: 0.8026 (t80) cc_final: 0.7683 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2254 time to fit residues: 29.7914 Evaluate side-chains 65 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 726 ASN B 863 ASN B1252 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14623 Z= 0.329 Angle : 0.619 11.586 20341 Z= 0.333 Chirality : 0.038 0.180 2319 Planarity : 0.004 0.065 2088 Dihedral : 21.479 108.210 3411 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.68 (0.23), residues: 1353 helix: 1.30 (0.20), residues: 687 sheet: -0.57 (0.62), residues: 70 loop : -0.35 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 464 HIS 0.007 0.002 HIS B1262 PHE 0.015 0.002 PHE B 970 TYR 0.020 0.002 TYR B 373 ARG 0.008 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9309 (mpp) cc_final: 0.8503 (ttt) REVERT: B 383 MET cc_start: 0.8304 (mmp) cc_final: 0.7963 (mmm) REVERT: B 534 MET cc_start: 0.6120 (mtp) cc_final: 0.5509 (ptm) REVERT: B 659 TRP cc_start: 0.8344 (m100) cc_final: 0.7820 (m100) REVERT: B 718 ASP cc_start: 0.9468 (m-30) cc_final: 0.9045 (p0) REVERT: B 781 MET cc_start: 0.9205 (mmm) cc_final: 0.8910 (mmm) REVERT: B 822 MET cc_start: 0.9319 (mmp) cc_final: 0.8703 (mmm) REVERT: B 1213 MET cc_start: 0.7456 (mmm) cc_final: 0.7234 (tpp) REVERT: B 1219 GLU cc_start: 0.8790 (tt0) cc_final: 0.8418 (tt0) REVERT: B 1242 TYR cc_start: 0.8159 (t80) cc_final: 0.7847 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2366 time to fit residues: 28.0081 Evaluate side-chains 57 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14623 Z= 0.255 Angle : 0.551 9.289 20341 Z= 0.299 Chirality : 0.036 0.170 2319 Planarity : 0.004 0.058 2088 Dihedral : 21.279 106.819 3411 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.82 (0.23), residues: 1353 helix: 1.45 (0.20), residues: 690 sheet: -0.59 (0.59), residues: 75 loop : -0.32 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 464 HIS 0.005 0.001 HIS B 595 PHE 0.012 0.002 PHE B 105 TYR 0.015 0.002 TYR B1265 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9263 (mpp) cc_final: 0.8753 (mpp) REVERT: B 383 MET cc_start: 0.8353 (mmp) cc_final: 0.8000 (mmm) REVERT: B 450 TYR cc_start: 0.7069 (m-80) cc_final: 0.6634 (m-10) REVERT: B 534 MET cc_start: 0.6049 (mtp) cc_final: 0.5488 (ptm) REVERT: B 659 TRP cc_start: 0.8384 (m100) cc_final: 0.7839 (m100) REVERT: B 718 ASP cc_start: 0.9518 (m-30) cc_final: 0.9124 (p0) REVERT: B 781 MET cc_start: 0.9189 (mmm) cc_final: 0.8898 (mmm) REVERT: B 822 MET cc_start: 0.9292 (mmp) cc_final: 0.8783 (mmm) REVERT: B 823 TYR cc_start: 0.8565 (m-80) cc_final: 0.8317 (m-10) REVERT: B 1213 MET cc_start: 0.7454 (mmm) cc_final: 0.7220 (tpp) REVERT: B 1219 GLU cc_start: 0.8814 (tt0) cc_final: 0.8452 (tt0) REVERT: B 1242 TYR cc_start: 0.8112 (t80) cc_final: 0.7806 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2212 time to fit residues: 26.6098 Evaluate side-chains 60 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 71 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14623 Z= 0.281 Angle : 0.581 9.335 20341 Z= 0.315 Chirality : 0.037 0.163 2319 Planarity : 0.004 0.053 2088 Dihedral : 21.345 107.516 3411 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.65 (0.23), residues: 1353 helix: 1.32 (0.20), residues: 692 sheet: -0.67 (0.60), residues: 75 loop : -0.43 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 464 HIS 0.007 0.001 HIS B1262 PHE 0.013 0.002 PHE B 97 TYR 0.017 0.002 TYR B 450 ARG 0.006 0.001 ARG B 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.438 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: B 90 MET cc_start: 0.9295 (mpp) cc_final: 0.8755 (mpp) REVERT: B 383 MET cc_start: 0.8368 (mmp) cc_final: 0.8030 (mmm) REVERT: B 534 MET cc_start: 0.6183 (mtp) cc_final: 0.5676 (ptm) REVERT: B 659 TRP cc_start: 0.8368 (m100) cc_final: 0.7883 (m100) REVERT: B 718 ASP cc_start: 0.9564 (m-30) cc_final: 0.9248 (p0) REVERT: B 781 MET cc_start: 0.9126 (mmm) cc_final: 0.8824 (mmm) REVERT: B 822 MET cc_start: 0.9295 (mmp) cc_final: 0.8788 (mmm) REVERT: B 823 TYR cc_start: 0.8620 (m-80) cc_final: 0.8331 (m-10) REVERT: B 1044 ASN cc_start: 0.9096 (m110) cc_final: 0.8689 (t0) REVERT: B 1213 MET cc_start: 0.7487 (mmm) cc_final: 0.7264 (tpp) REVERT: B 1219 GLU cc_start: 0.8799 (tt0) cc_final: 0.8465 (tt0) REVERT: B 1242 TYR cc_start: 0.8133 (t80) cc_final: 0.7851 (t80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2408 time to fit residues: 27.6583 Evaluate side-chains 58 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.056189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041676 restraints weight = 130754.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.042915 restraints weight = 69756.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.043638 restraints weight = 47484.000| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14623 Z= 0.203 Angle : 0.513 7.524 20341 Z= 0.279 Chirality : 0.035 0.172 2319 Planarity : 0.004 0.050 2088 Dihedral : 21.101 105.782 3411 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.99 (0.23), residues: 1353 helix: 1.68 (0.20), residues: 682 sheet: -0.55 (0.60), residues: 75 loop : -0.34 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 464 HIS 0.006 0.001 HIS B 595 PHE 0.011 0.001 PHE B 105 TYR 0.013 0.001 TYR B1265 ARG 0.005 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.29 seconds wall clock time: 47 minutes 32.29 seconds (2852.29 seconds total)