Starting phenix.real_space_refine on Sun Nov 17 16:29:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqh_40705/11_2024/8sqh_40705.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 146 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8430 2.51 5 N 2476 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14101 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 11002 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 36, 'TRANS': 1304} Chain breaks: 3 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "c" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.18, per 1000 atoms: 0.65 Number of scatterers: 14101 At special positions: 0 Unit cell: (85.54, 119.38, 130.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 146 15.00 Mg 4 11.99 O 3023 8.00 N 2476 7.00 C 8430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 11 sheets defined 53.8% alpha, 10.0% beta 54 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.997A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.568A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.607A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.510A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.371A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.807A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.738A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.623A pdb=" N ASN A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.600A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.397A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.550A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.844A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.354A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.603A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.717A pdb=" N GLN A 805 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.679A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.142A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.398A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.652A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.377A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.519A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1298 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 4.148A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.290A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.587A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.904A pdb=" N PHE A 252 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.702A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AB1, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.752A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1326 515 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3719 1.34 - 1.46: 3699 1.46 - 1.58: 6914 1.58 - 1.70: 286 1.70 - 1.82: 42 Bond restraints: 14660 Sorted by residual: bond pdb=" CA ASP A 585 " pdb=" CB ASP A 585 " ideal model delta sigma weight residual 1.530 1.567 -0.037 1.69e-02 3.50e+03 4.68e+00 bond pdb=" O5' DG c 12 " pdb=" C5' DG c 12 " ideal model delta sigma weight residual 1.423 1.360 0.063 3.00e-02 1.11e+03 4.38e+00 bond pdb=" O5' DT c 9 " pdb=" C5' DT c 9 " ideal model delta sigma weight residual 1.423 1.363 0.060 3.00e-02 1.11e+03 4.02e+00 bond pdb=" C1' DC c 6 " pdb=" N1 DC c 6 " ideal model delta sigma weight residual 1.490 1.550 -0.060 3.00e-02 1.11e+03 4.01e+00 bond pdb=" CB PRO A 800 " pdb=" CG PRO A 800 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.68e+00 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 19846 2.94 - 5.88: 462 5.88 - 8.82: 77 8.82 - 11.76: 18 11.76 - 14.70: 7 Bond angle restraints: 20410 Sorted by residual: angle pdb=" O3' G B 11 " pdb=" C3' G B 11 " pdb=" C2' G B 11 " ideal model delta sigma weight residual 113.70 122.01 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" CB LYS A1158 " pdb=" CG LYS A1158 " pdb=" CD LYS A1158 " ideal model delta sigma weight residual 111.30 123.40 -12.10 2.30e+00 1.89e-01 2.77e+01 angle pdb=" CA ASP A 585 " pdb=" CB ASP A 585 " pdb=" CG ASP A 585 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" C2' A B 8 " pdb=" C1' A B 8 " pdb=" N9 A B 8 " ideal model delta sigma weight residual 112.00 119.70 -7.70 1.50e+00 4.44e-01 2.63e+01 angle pdb=" CB LYS A 775 " pdb=" CG LYS A 775 " pdb=" CD LYS A 775 " ideal model delta sigma weight residual 111.30 123.03 -11.73 2.30e+00 1.89e-01 2.60e+01 ... (remaining 20405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 8202 29.86 - 59.71: 571 59.71 - 89.57: 115 89.57 - 119.42: 3 119.42 - 149.28: 2 Dihedral angle restraints: 8893 sinusoidal: 4949 harmonic: 3944 Sorted by residual: dihedral pdb=" CA SER A1106 " pdb=" C SER A1106 " pdb=" N LYS A1107 " pdb=" CA LYS A1107 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP A 837 " pdb=" C ASP A 837 " pdb=" N VAL A 838 " pdb=" CA VAL A 838 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS A 526 " pdb=" C LYS A 526 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 8890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2235 0.127 - 0.255: 87 0.255 - 0.382: 10 0.382 - 0.510: 1 0.510 - 0.637: 4 Chirality restraints: 2337 Sorted by residual: chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.48 -1.84 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C4' A B 12 " pdb=" C5' A B 12 " pdb=" O4' A B 12 " pdb=" C3' A B 12 " both_signs ideal model delta sigma weight residual False -2.50 -1.86 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C3' G B 11 " pdb=" C4' G B 11 " pdb=" O3' G B 11 " pdb=" C2' G B 11 " both_signs ideal model delta sigma weight residual False -2.48 -1.89 -0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 2334 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 41 " -0.063 2.00e-02 2.50e+03 2.90e-02 2.53e+01 pdb=" N9 DG D 41 " 0.075 2.00e-02 2.50e+03 pdb=" C8 DG D 41 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 41 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG D 41 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG D 41 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG D 41 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG D 41 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG D 41 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG D 41 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 41 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG D 41 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " 0.040 2.00e-02 2.50e+03 2.88e-02 2.49e+01 pdb=" N9 G B 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G B 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 1 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT c 11 " 0.026 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" N1 DT c 11 " -0.074 2.00e-02 2.50e+03 pdb=" C2 DT c 11 " 0.047 2.00e-02 2.50e+03 pdb=" O2 DT c 11 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT c 11 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DT c 11 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT c 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT c 11 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT c 11 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT c 11 " 0.006 2.00e-02 2.50e+03 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 79 2.54 - 3.13: 10533 3.13 - 3.72: 24467 3.72 - 4.31: 32720 4.31 - 4.90: 50396 Nonbonded interactions: 118195 Sorted by model distance: nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1402 " model vdw 1.955 2.170 nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1401 " model vdw 2.015 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1402 " model vdw 2.040 2.250 nonbonded pdb=" OE1 GLU A 762 " pdb="MG MG A1401 " model vdw 2.045 2.170 nonbonded pdb=" OP2 A B 65 " pdb="MG MG B 101 " model vdw 2.062 2.170 ... (remaining 118190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 40.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.005 0.096 14660 Z= 0.327 Angle : 1.119 14.698 20410 Z= 0.609 Chirality : 0.064 0.637 2337 Planarity : 0.008 0.083 2074 Dihedral : 19.150 149.280 6339 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.17 % Allowed : 17.78 % Favored : 82.05 % Cbeta Deviations : 0.08 % 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: -1.51 (0.21), residues: 1333 helix: -1.07 (0.18), residues: 629 sheet: -0.29 (0.64), residues: 80 loop : -0.86 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1136 HIS 0.010 0.002 HIS A 167 PHE 0.033 0.002 PHE A1046 TYR 0.033 0.004 TYR A 192 ARG 0.039 0.003 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1325 LYS cc_start: 0.9228 (ptmt) cc_final: 0.8750 (ttpp) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.3124 time to fit residues: 24.0214 Evaluate side-chains 42 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 921 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14660 Z= 0.246 Angle : 0.612 8.668 20410 Z= 0.328 Chirality : 0.039 0.235 2337 Planarity : 0.004 0.044 2074 Dihedral : 19.506 156.514 3465 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.23 % Allowed : 14.06 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1333 helix: 0.33 (0.20), residues: 643 sheet: 0.06 (0.51), residues: 106 loop : -0.22 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1136 HIS 0.005 0.001 HIS A 412 PHE 0.012 0.001 PHE A1046 TYR 0.023 0.001 TYR A 192 ARG 0.005 0.001 ARG A1171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 1.454 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: A 196 PHE cc_start: 0.9684 (t80) cc_final: 0.9483 (t80) REVERT: A 647 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9167 (m) REVERT: A 974 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8803 (ptmt) outliers start: 27 outliers final: 6 residues processed: 70 average time/residue: 0.3271 time to fit residues: 33.5420 Evaluate side-chains 49 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1328 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14660 Z= 0.399 Angle : 0.676 11.281 20410 Z= 0.356 Chirality : 0.041 0.181 2337 Planarity : 0.004 0.047 2074 Dihedral : 19.654 159.859 3465 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.48 % Allowed : 14.72 % Favored : 82.80 % 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 (0.23), residues: 1333 helix: 0.53 (0.20), residues: 635 sheet: 0.16 (0.51), residues: 104 loop : -0.14 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.012 0.002 HIS A 328 PHE 0.013 0.002 PHE A 164 TYR 0.017 0.002 TYR A 192 ARG 0.007 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9694 (t80) cc_final: 0.9479 (t80) REVERT: A 804 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8409 (t) REVERT: A 807 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8880 (mp10) REVERT: A 974 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8719 (ptmt) outliers start: 30 outliers final: 11 residues processed: 75 average time/residue: 0.2994 time to fit residues: 33.2087 Evaluate side-chains 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14660 Z= 0.261 Angle : 0.575 12.069 20410 Z= 0.304 Chirality : 0.037 0.181 2337 Planarity : 0.003 0.046 2074 Dihedral : 19.521 158.273 3465 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.07 % Allowed : 15.05 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1333 helix: 0.88 (0.20), residues: 630 sheet: 0.20 (0.52), residues: 104 loop : -0.08 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.011 0.001 PHE A 575 TYR 0.017 0.001 TYR A 155 ARG 0.005 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9684 (t80) cc_final: 0.9467 (t80) REVERT: A 261 ASP cc_start: 0.0630 (OUTLIER) cc_final: -0.0664 (t0) REVERT: A 664 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8945 (tmm-80) REVERT: A 781 MET cc_start: 0.8616 (tpp) cc_final: 0.8395 (tpp) REVERT: A 974 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8667 (ptmt) outliers start: 25 outliers final: 11 residues processed: 66 average time/residue: 0.3112 time to fit residues: 30.2072 Evaluate side-chains 56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14660 Z= 0.163 Angle : 0.515 10.882 20410 Z= 0.274 Chirality : 0.036 0.181 2337 Planarity : 0.003 0.043 2074 Dihedral : 19.334 155.051 3465 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.57 % Allowed : 16.21 % Favored : 82.22 % 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: 0.79 (0.24), residues: 1333 helix: 1.14 (0.21), residues: 632 sheet: 0.34 (0.52), residues: 106 loop : 0.01 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 PHE 0.010 0.001 PHE A 575 TYR 0.016 0.001 TYR A 192 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9676 (t80) cc_final: 0.9458 (t80) REVERT: A 261 ASP cc_start: 0.0449 (OUTLIER) cc_final: -0.0877 (t0) REVERT: A 294 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8967 (tmtt) REVERT: A 807 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8926 (mp10) REVERT: A 974 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8638 (ptmt) REVERT: A 1325 LYS cc_start: 0.9328 (ptmt) cc_final: 0.8999 (tttm) outliers start: 19 outliers final: 14 residues processed: 62 average time/residue: 0.3097 time to fit residues: 29.4570 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14660 Z= 0.206 Angle : 0.533 12.808 20410 Z= 0.280 Chirality : 0.036 0.178 2337 Planarity : 0.003 0.042 2074 Dihedral : 19.331 156.460 3465 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.90 % Allowed : 16.87 % Favored : 81.22 % 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: 0.75 (0.23), residues: 1333 helix: 1.14 (0.21), residues: 636 sheet: 0.44 (0.52), residues: 104 loop : -0.08 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.009 0.001 PHE A 575 TYR 0.014 0.001 TYR A 192 ARG 0.003 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9671 (t80) cc_final: 0.9458 (t80) REVERT: A 218 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8784 (mmmt) REVERT: A 261 ASP cc_start: 0.0499 (OUTLIER) cc_final: -0.0806 (t0) REVERT: A 294 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8986 (tmtt) REVERT: A 664 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8915 (tmm-80) REVERT: A 974 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8471 (ptmt) outliers start: 23 outliers final: 17 residues processed: 63 average time/residue: 0.3331 time to fit residues: 30.8369 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 0.0010 chunk 64 optimal weight: 5.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14660 Z= 0.183 Angle : 0.527 13.207 20410 Z= 0.276 Chirality : 0.036 0.180 2337 Planarity : 0.003 0.041 2074 Dihedral : 19.313 155.741 3465 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 16.96 % Favored : 80.98 % 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: 0.80 (0.23), residues: 1333 helix: 1.19 (0.21), residues: 635 sheet: 0.51 (0.52), residues: 106 loop : -0.08 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.009 0.001 PHE A 575 TYR 0.015 0.001 TYR A 192 ARG 0.002 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 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: A 196 PHE cc_start: 0.9665 (t80) cc_final: 0.9451 (t80) REVERT: A 261 ASP cc_start: 0.0674 (OUTLIER) cc_final: -0.0642 (t0) REVERT: A 294 LYS cc_start: 0.9321 (tmtt) cc_final: 0.9052 (tmtt) REVERT: A 664 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.8902 (tmm-80) REVERT: A 974 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8482 (ptmt) outliers start: 25 outliers final: 19 residues processed: 66 average time/residue: 0.3457 time to fit residues: 33.1833 Evaluate side-chains 63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14660 Z= 0.184 Angle : 0.530 13.435 20410 Z= 0.275 Chirality : 0.036 0.197 2337 Planarity : 0.003 0.041 2074 Dihedral : 19.303 155.750 3465 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.23 % Allowed : 17.12 % Favored : 80.65 % 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: 0.84 (0.23), residues: 1333 helix: 1.24 (0.21), residues: 635 sheet: 0.52 (0.52), residues: 106 loop : -0.08 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.008 0.001 PHE A 575 TYR 0.014 0.001 TYR A 192 ARG 0.002 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9659 (t80) cc_final: 0.9445 (t80) REVERT: A 261 ASP cc_start: 0.0517 (OUTLIER) cc_final: -0.0795 (t0) REVERT: A 294 LYS cc_start: 0.9359 (tmtt) cc_final: 0.9095 (tmtt) REVERT: A 664 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.8899 (tmm-80) REVERT: A 974 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8482 (ptmt) REVERT: A 1325 LYS cc_start: 0.9380 (ptmt) cc_final: 0.9094 (tttm) outliers start: 27 outliers final: 22 residues processed: 66 average time/residue: 0.3459 time to fit residues: 33.3269 Evaluate side-chains 65 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14660 Z= 0.147 Angle : 0.523 12.317 20410 Z= 0.272 Chirality : 0.035 0.211 2337 Planarity : 0.003 0.039 2074 Dihedral : 19.269 154.289 3465 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 17.54 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1333 helix: 1.24 (0.21), residues: 636 sheet: 0.59 (0.52), residues: 106 loop : -0.04 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.007 0.001 PHE A 575 TYR 0.015 0.001 TYR A 192 ARG 0.004 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9662 (t80) cc_final: 0.9446 (t80) REVERT: A 218 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8744 (mmmt) REVERT: A 261 ASP cc_start: 0.0628 (OUTLIER) cc_final: -0.0705 (t0) REVERT: A 294 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9101 (tmtt) REVERT: A 648 MET cc_start: 0.9571 (ttp) cc_final: 0.9286 (tpp) REVERT: A 664 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8903 (tmm-80) REVERT: A 781 MET cc_start: 0.8625 (tpp) cc_final: 0.8349 (tpp) REVERT: A 974 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8488 (ptmt) outliers start: 23 outliers final: 18 residues processed: 62 average time/residue: 0.3402 time to fit residues: 30.8115 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14660 Z= 0.211 Angle : 0.548 12.322 20410 Z= 0.284 Chirality : 0.036 0.210 2337 Planarity : 0.003 0.040 2074 Dihedral : 19.317 156.309 3465 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.65 % Allowed : 17.87 % Favored : 80.48 % 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: 0.91 (0.24), residues: 1333 helix: 1.26 (0.21), residues: 637 sheet: 0.62 (0.52), residues: 104 loop : -0.02 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.008 0.001 PHE A 446 TYR 0.014 0.001 TYR A 192 ARG 0.002 0.000 ARG A 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9657 (t80) cc_final: 0.9441 (t80) REVERT: A 218 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8764 (mmmt) REVERT: A 261 ASP cc_start: 0.0603 (OUTLIER) cc_final: 0.0084 (t70) REVERT: A 294 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9152 (tmtt) REVERT: A 664 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8885 (tmm-80) REVERT: A 781 MET cc_start: 0.8651 (tpp) cc_final: 0.8392 (tpp) REVERT: A 974 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8455 (ptmt) REVERT: A 1325 LYS cc_start: 0.9381 (ptmt) cc_final: 0.9068 (tttm) outliers start: 20 outliers final: 17 residues processed: 58 average time/residue: 0.3468 time to fit residues: 29.2788 Evaluate side-chains 58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.043116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.032501 restraints weight = 94203.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.033518 restraints weight = 46484.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034174 restraints weight = 30570.888| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14660 Z= 0.159 Angle : 0.529 11.611 20410 Z= 0.274 Chirality : 0.035 0.210 2337 Planarity : 0.003 0.040 2074 Dihedral : 19.296 154.621 3465 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 17.95 % Favored : 80.40 % 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: 0.96 (0.24), residues: 1333 helix: 1.31 (0.21), residues: 635 sheet: 0.63 (0.52), residues: 106 loop : 0.01 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 PHE 0.007 0.001 PHE A 575 TYR 0.014 0.001 TYR A 192 ARG 0.009 0.000 ARG A 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.03 seconds wall clock time: 42 minutes 8.52 seconds (2528.52 seconds total)