Starting phenix.real_space_refine on Thu Jun 12 17:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_40705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_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/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_40705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_40705.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_40705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqh_40705/06_2025/8sqh_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.15, 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: 3.78 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: 5.57 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: 7.82 Time building geometry restraints manager: 4.41 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.720 Find NCS groups from input model: 0.130 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.500 ------------------------------------------------------------------------------- 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= 0.250 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 Details of bonding type rmsd hydrogen bonds : bond 0.13845 ( 636) hydrogen bonds : angle 6.07353 ( 1729) covalent geometry : bond 0.00542 (14660) covalent geometry : angle 1.11930 (20410) *********************** 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 : 1.425 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: 0.3108 time to fit residues: 23.7942 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 : 1.800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.033224 restraints weight = 90864.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.034295 restraints weight = 43634.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.035004 restraints weight = 28419.480| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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= 0.186 Angle : 0.612 8.668 20410 Z= 0.328 Chirality : 0.039 0.235 2337 Planarity : 0.004 0.044 2074 Dihedral : 19.506 156.515 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 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 636) hydrogen bonds : angle 4.72113 ( 1729) covalent geometry : bond 0.00395 (14660) covalent geometry : angle 0.61155 (20410) *********************** 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 : 1.492 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: 0.9672 (t80) cc_final: 0.9466 (t80) REVERT: A 647 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9135 (m) REVERT: A 974 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8904 (ptmt) outliers start: 27 outliers final: 6 residues processed: 70 average time/residue: 0.3212 time to fit residues: 32.8321 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 : 1.479 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 A1208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031304 restraints weight = 94002.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.032335 restraints weight = 45067.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.033008 restraints weight = 29433.078| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14660 Z= 0.220 Angle : 0.600 12.591 20410 Z= 0.318 Chirality : 0.038 0.183 2337 Planarity : 0.004 0.046 2074 Dihedral : 19.513 157.405 3465 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.40 % Allowed : 14.31 % Favored : 83.29 % 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: 0.42 (0.23), residues: 1333 helix: 0.67 (0.20), residues: 643 sheet: 0.19 (0.51), residues: 106 loop : 0.01 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1136 HIS 0.011 0.001 HIS A 328 PHE 0.011 0.002 PHE A 575 TYR 0.017 0.001 TYR A 192 ARG 0.009 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 636) hydrogen bonds : angle 4.49667 ( 1729) covalent geometry : bond 0.00469 (14660) covalent geometry : angle 0.59990 (20410) *********************** 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 73 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9689 (t80) cc_final: 0.9469 (t80) REVERT: A 585 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8315 (p0) REVERT: A 804 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8362 (t) REVERT: A 807 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8874 (mp10) REVERT: A 974 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8838 (ptmt) REVERT: A 1325 LYS cc_start: 0.9306 (ptmt) cc_final: 0.8935 (tttm) outliers start: 29 outliers final: 10 residues processed: 71 average time/residue: 0.3018 time to fit residues: 31.8578 Evaluate side-chains 55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 585 ASP 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 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 49 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** A1208 ASN ** A1261 GLN ** 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 = 0.2966 r_free = 0.2966 target = 0.041149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.030473 restraints weight = 95420.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031451 restraints weight = 45718.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.032055 restraints weight = 29877.102| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14660 Z= 0.268 Angle : 0.626 11.721 20410 Z= 0.330 Chirality : 0.039 0.179 2337 Planarity : 0.004 0.046 2074 Dihedral : 19.524 160.209 3465 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 14.56 % Favored : 82.71 % 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: 0.44 (0.23), residues: 1333 helix: 0.81 (0.20), residues: 632 sheet: 0.18 (0.51), residues: 104 loop : -0.13 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.009 0.001 HIS A 328 PHE 0.013 0.002 PHE A 575 TYR 0.018 0.002 TYR A 155 ARG 0.009 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 636) hydrogen bonds : angle 4.49401 ( 1729) covalent geometry : bond 0.00565 (14660) covalent geometry : angle 0.62634 (20410) *********************** 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 74 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9689 (t80) cc_final: 0.9477 (t80) REVERT: A 261 ASP cc_start: 0.0480 (OUTLIER) cc_final: -0.0679 (t0) REVERT: A 294 LYS cc_start: 0.9265 (tmtt) cc_final: 0.9007 (tmtt) REVERT: A 664 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.8937 (tmm-80) REVERT: A 974 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8738 (ptmt) REVERT: A 1006 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8757 (t) outliers start: 33 outliers final: 15 residues processed: 71 average time/residue: 0.3155 time to fit residues: 33.1329 Evaluate side-chains 58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ASP 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 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 975 VAL Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1014 LYS 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 1328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.030751 restraints weight = 94341.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031775 restraints weight = 44016.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032411 restraints weight = 28405.854| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14660 Z= 0.184 Angle : 0.559 12.385 20410 Z= 0.296 Chirality : 0.037 0.181 2337 Planarity : 0.003 0.045 2074 Dihedral : 19.479 158.112 3465 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.82 % Allowed : 16.21 % Favored : 81.97 % 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: 0.60 (0.23), residues: 1333 helix: 0.95 (0.21), residues: 638 sheet: 0.21 (0.51), residues: 104 loop : -0.05 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.010 0.001 PHE A 575 TYR 0.017 0.001 TYR A 155 ARG 0.003 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 636) hydrogen bonds : angle 4.30476 ( 1729) covalent geometry : bond 0.00392 (14660) covalent geometry : angle 0.55914 (20410) *********************** 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 65 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9699 (t80) cc_final: 0.9486 (t80) REVERT: A 261 ASP cc_start: 0.0565 (OUTLIER) cc_final: -0.0694 (t0) REVERT: A 294 LYS cc_start: 0.9305 (tmtt) cc_final: 0.9033 (tmtt) REVERT: A 495 MET cc_start: 0.9105 (ttm) cc_final: 0.8844 (ttm) REVERT: A 974 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8695 (ptmt) outliers start: 22 outliers final: 16 residues processed: 62 average time/residue: 0.2857 time to fit residues: 26.8803 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 244 LEU 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 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 975 VAL Chi-restraints excluded: chain A residue 1006 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 128 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** A1224 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.030918 restraints weight = 95127.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031942 restraints weight = 44350.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032592 restraints weight = 28580.760| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14660 Z= 0.174 Angle : 0.541 9.939 20410 Z= 0.287 Chirality : 0.037 0.178 2337 Planarity : 0.003 0.044 2074 Dihedral : 19.415 157.406 3465 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 2.23 % Allowed : 16.38 % Favored : 81.39 % 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: 1.13 (0.21), residues: 631 sheet: 0.22 (0.51), residues: 104 loop : -0.02 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.010 0.001 PHE A 575 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 636) hydrogen bonds : angle 4.19624 ( 1729) covalent geometry : bond 0.00370 (14660) covalent geometry : angle 0.54089 (20410) *********************** 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 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 42 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9690 (t80) cc_final: 0.9481 (t80) REVERT: A 261 ASP cc_start: 0.0578 (OUTLIER) cc_final: 0.0080 (t70) REVERT: A 294 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9114 (tmtt) REVERT: A 495 MET cc_start: 0.9120 (ttm) cc_final: 0.8864 (ttm) REVERT: A 664 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.8894 (tmm-80) REVERT: A 763 MET cc_start: 0.9246 (tpp) cc_final: 0.8968 (tpp) REVERT: A 781 MET cc_start: 0.8759 (tpp) cc_final: 0.8473 (tpp) REVERT: A 974 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8569 (ptmt) REVERT: A 1325 LYS cc_start: 0.9323 (ptmt) cc_final: 0.9063 (tttm) outliers start: 27 outliers final: 18 residues processed: 68 average time/residue: 0.3039 time to fit residues: 30.6031 Evaluate side-chains 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ASP 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 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 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 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 1360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** ** A1224 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031324 restraints weight = 93984.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032350 restraints weight = 43766.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.033006 restraints weight = 28305.846| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14660 Z= 0.135 Angle : 0.519 8.067 20410 Z= 0.276 Chirality : 0.036 0.179 2337 Planarity : 0.003 0.043 2074 Dihedral : 19.370 155.879 3465 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 1.74 % Allowed : 17.29 % 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: 0.90 (0.23), residues: 1333 helix: 1.27 (0.21), residues: 629 sheet: 0.32 (0.52), residues: 104 loop : 0.03 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 PHE 0.008 0.001 PHE A 575 TYR 0.015 0.001 TYR A 192 ARG 0.002 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 636) hydrogen bonds : angle 4.08400 ( 1729) covalent geometry : bond 0.00288 (14660) covalent geometry : angle 0.51863 (20410) *********************** 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 62 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 1.394 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: 0.9690 (t80) cc_final: 0.9481 (t80) REVERT: A 294 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9125 (tmtt) REVERT: A 495 MET cc_start: 0.9115 (ttm) cc_final: 0.8850 (ttm) REVERT: A 664 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8919 (tmm-80) REVERT: A 763 MET cc_start: 0.9244 (tpp) cc_final: 0.8885 (tpp) REVERT: A 781 MET cc_start: 0.8704 (tpp) cc_final: 0.8466 (tpp) REVERT: A 974 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8539 (ptmt) REVERT: A 1325 LYS cc_start: 0.9336 (ptmt) cc_final: 0.9086 (tttm) outliers start: 21 outliers final: 17 residues processed: 61 average time/residue: 0.3228 time to fit residues: 28.7531 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 244 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 190 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.029672 restraints weight = 97683.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.030618 restraints weight = 46664.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031257 restraints weight = 30560.557| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 14660 Z= 0.320 Angle : 0.663 10.795 20410 Z= 0.345 Chirality : 0.040 0.196 2337 Planarity : 0.004 0.045 2074 Dihedral : 19.564 161.464 3465 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.23 % Allowed : 17.45 % Favored : 80.31 % 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: 0.44 (0.23), residues: 1333 helix: 0.91 (0.21), residues: 636 sheet: 0.16 (0.51), residues: 104 loop : -0.25 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.008 0.001 HIS A 328 PHE 0.013 0.002 PHE A 446 TYR 0.020 0.002 TYR A 155 ARG 0.004 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 636) hydrogen bonds : angle 4.46055 ( 1729) covalent geometry : bond 0.00673 (14660) covalent geometry : angle 0.66319 (20410) *********************** 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 68 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9700 (t80) cc_final: 0.9490 (t80) REVERT: A 261 ASP cc_start: 0.0300 (OUTLIER) cc_final: -0.0234 (t70) REVERT: A 294 LYS cc_start: 0.9405 (tmtt) cc_final: 0.9174 (tmtt) REVERT: A 495 MET cc_start: 0.9093 (ttm) cc_final: 0.8836 (ttm) REVERT: A 664 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8843 (tmm-80) REVERT: A 974 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8491 (ptmt) REVERT: A 1325 LYS cc_start: 0.9379 (ptmt) cc_final: 0.9119 (tttt) outliers start: 27 outliers final: 21 residues processed: 66 average time/residue: 0.3198 time to fit residues: 31.2146 Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP 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 648 MET 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 789 LYS 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 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 131 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** A1224 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031216 restraints weight = 93581.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032232 restraints weight = 43721.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.032902 restraints weight = 28268.716| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14660 Z= 0.120 Angle : 0.541 8.251 20410 Z= 0.285 Chirality : 0.036 0.212 2337 Planarity : 0.003 0.042 2074 Dihedral : 19.428 155.576 3465 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.82 % Allowed : 17.70 % 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: 0.87 (0.24), residues: 1333 helix: 1.28 (0.21), residues: 629 sheet: 0.21 (0.51), residues: 106 loop : -0.01 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 883 HIS 0.005 0.001 HIS A 167 PHE 0.008 0.001 PHE A 575 TYR 0.015 0.001 TYR A 192 ARG 0.003 0.000 ARG A 535 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 636) hydrogen bonds : angle 4.10623 ( 1729) covalent geometry : bond 0.00259 (14660) covalent geometry : angle 0.54125 (20410) *********************** 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: 22 poor density : 42 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.0364 (OUTLIER) cc_final: -0.0251 (t70) REVERT: A 294 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9180 (tmtt) REVERT: A 495 MET cc_start: 0.9086 (ttm) cc_final: 0.8870 (ttm) REVERT: A 664 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8939 (tmm-80) REVERT: A 974 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8519 (ptmt) REVERT: A 1325 LYS cc_start: 0.9325 (ptmt) cc_final: 0.9060 (tttm) outliers start: 22 outliers final: 14 residues processed: 61 average time/residue: 0.3217 time to fit residues: 28.8162 Evaluate side-chains 56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 290 PHE 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** A1224 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.031092 restraints weight = 93904.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.032092 restraints weight = 43916.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.032765 restraints weight = 28354.715| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14660 Z= 0.141 Angle : 0.566 13.839 20410 Z= 0.293 Chirality : 0.036 0.226 2337 Planarity : 0.003 0.042 2074 Dihedral : 19.390 155.985 3465 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.57 % Allowed : 18.28 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1333 helix: 1.33 (0.21), residues: 629 sheet: 0.38 (0.52), residues: 104 loop : -0.06 (0.27), residues: 600 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 0.020 0.001 TYR A 192 ARG 0.003 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 636) hydrogen bonds : angle 4.05501 ( 1729) covalent geometry : bond 0.00306 (14660) covalent geometry : angle 0.56595 (20410) ********************** 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 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.8770 (tp) cc_final: 0.8433 (mt) REVERT: A 261 ASP cc_start: 0.0554 (OUTLIER) cc_final: -0.0044 (t70) REVERT: A 294 LYS cc_start: 0.9431 (tmtt) cc_final: 0.9191 (tmtt) REVERT: A 495 MET cc_start: 0.9089 (ttm) cc_final: 0.8878 (ttm) REVERT: A 664 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8894 (tmm-80) REVERT: A 974 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8490 (ptmt) REVERT: A 1325 LYS cc_start: 0.9331 (ptmt) cc_final: 0.9060 (tttm) outliers start: 19 outliers final: 14 residues processed: 59 average time/residue: 0.3355 time to fit residues: 29.3192 Evaluate side-chains 58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 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 789 LYS 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 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.029733 restraints weight = 98571.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030690 restraints weight = 47121.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031317 restraints weight = 30593.589| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 14660 Z= 0.317 Angle : 0.686 14.003 20410 Z= 0.356 Chirality : 0.040 0.220 2337 Planarity : 0.004 0.046 2074 Dihedral : 19.567 161.085 3465 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.90 % Allowed : 17.95 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1333 helix: 0.99 (0.21), residues: 636 sheet: 0.15 (0.51), residues: 104 loop : -0.32 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.008 0.001 HIS A 328 PHE 0.019 0.002 PHE A 196 TYR 0.020 0.002 TYR A 155 ARG 0.008 0.001 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 636) hydrogen bonds : angle 4.40189 ( 1729) covalent geometry : bond 0.00667 (14660) covalent geometry : angle 0.68571 (20410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.68 seconds wall clock time: 72 minutes 9.78 seconds (4329.78 seconds total)