Starting phenix.real_space_refine on Mon Jul 28 23:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.map" model { file = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2025/8t77_41086.cif" } resolution = 3.25 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 114 5.49 5 S 16 5.16 5 C 6427 2.51 5 N 1889 2.21 5 O 2299 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-5711/modules/chem_data/mon_lib" Total number of atoms: 10745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8328 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 27, 'TRANS': 997} Chain breaks: 8 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1905 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 7.73, per 1000 atoms: 0.72 Number of scatterers: 10745 At special positions: 0 Unit cell: (85.8196, 120.814, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 114 15.00 O 2299 8.00 N 1889 7.00 C 6427 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 55.7% alpha, 7.3% beta 35 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.650A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (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: 3.828A 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 196 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.585A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) 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 removed outlier: 3.568A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.187A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.192A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.597A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.615A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.999A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.274A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.743A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 4.135A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.526A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 removed outlier: 3.603A pdb=" N LYS A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.701A 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 710 removed outlier: 4.151A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.008A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.893A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.663A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.738A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 999 removed outlier: 4.776A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.501A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.819A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (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 removed outlier: 3.831A pdb=" N SER A1240 " --> pdb=" O LEU A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1246 Processing helix chain 'A' and resid 1251 through 1261 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.676A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.655A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 8 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 49 " --> pdb=" O TRP A 18 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.174A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.924A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1325 360 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2297 1.33 - 1.45: 2911 1.45 - 1.57: 5718 1.57 - 1.69: 226 1.69 - 1.81: 30 Bond restraints: 11182 Sorted by residual: bond pdb=" CB ASP A 406 " pdb=" CG ASP A 406 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CB GLN A1091 " pdb=" CG GLN A1091 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB ASP A 384 " pdb=" CG ASP A 384 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.82e+00 bond pdb=" CB GLU A 470 " pdb=" CG GLU A 470 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CG GLN A1091 " pdb=" CD GLN A1091 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.29e+00 ... (remaining 11177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 15345 3.20 - 6.40: 217 6.40 - 9.61: 28 9.61 - 12.81: 8 12.81 - 16.01: 2 Bond angle restraints: 15600 Sorted by residual: angle pdb=" CA LEU A 651 " pdb=" CB LEU A 651 " pdb=" CG LEU A 651 " ideal model delta sigma weight residual 116.30 132.31 -16.01 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CA LEU A1282 " pdb=" CB LEU A1282 " pdb=" CG LEU A1282 " ideal model delta sigma weight residual 116.30 132.29 -15.99 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CB GLN A1091 " pdb=" CG GLN A1091 " pdb=" CD GLN A1091 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CB LYS A 999 " pdb=" CG LYS A 999 " pdb=" CD LYS A 999 " ideal model delta sigma weight residual 111.30 120.61 -9.31 2.30e+00 1.89e-01 1.64e+01 angle pdb=" CA LYS A 999 " pdb=" CB LYS A 999 " pdb=" CG LYS A 999 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 ... (remaining 15595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 6266 30.44 - 60.88: 452 60.88 - 91.32: 79 91.32 - 121.77: 3 121.77 - 152.21: 2 Dihedral angle restraints: 6802 sinusoidal: 3786 harmonic: 3016 Sorted by residual: dihedral pdb=" CA TRP A 464 " pdb=" C TRP A 464 " pdb=" N MET A 465 " pdb=" CA MET A 465 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LYS A1107 " pdb=" C LYS A1107 " pdb=" N GLU A1108 " pdb=" CA GLU A1108 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A1259 " pdb=" C VAL A1259 " pdb=" N GLU A1260 " pdb=" CA GLU A1260 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1591 0.078 - 0.155: 206 0.155 - 0.233: 16 0.233 - 0.310: 3 0.310 - 0.388: 4 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB ILE A1352 " pdb=" CA ILE A1352 " pdb=" CG1 ILE A1352 " pdb=" CG2 ILE A1352 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CG LEU A 597 " pdb=" CB LEU A 597 " pdb=" CD1 LEU A 597 " pdb=" CD2 LEU A 597 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1' DC D 44 " pdb=" O4' DC D 44 " pdb=" C2' DC D 44 " pdb=" N1 DC D 44 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1817 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 19 " -0.022 2.00e-02 2.50e+03 2.40e-02 1.73e+01 pdb=" N9 G B 19 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G B 19 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 19 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 19 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G B 19 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G B 19 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G B 19 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 19 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1276 " 0.024 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE A1276 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A1276 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1276 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A1276 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1276 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A1276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " 0.023 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR A 517 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.007 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 442 2.70 - 3.25: 10213 3.25 - 3.80: 18734 3.80 - 4.35: 23697 4.35 - 4.90: 35637 Nonbonded interactions: 88723 Sorted by model distance: nonbonded pdb=" O GLY A 736 " pdb=" OG1 THR A 740 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP A1267 " pdb=" OH TYR A1294 " model vdw 2.245 3.040 nonbonded pdb=" O LEU A 455 " pdb=" O2' G B 58 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A1102 " pdb=" OP2 U B 64 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.295 3.040 ... (remaining 88718 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 individual isotropic 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: 15.580 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 0.055 11182 Z= 0.213 Angle : 0.990 16.010 15600 Z= 0.509 Chirality : 0.054 0.388 1820 Planarity : 0.007 0.082 1561 Dihedral : 19.381 152.208 4842 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 21.18 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1008 helix: -1.21 (0.20), residues: 502 sheet: -0.24 (0.51), residues: 110 loop : -0.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP A 18 HIS 0.015 0.002 HIS A 137 PHE 0.068 0.003 PHE A1276 TYR 0.068 0.004 TYR A 517 ARG 0.021 0.001 ARG A1111 Details of bonding type rmsd hydrogen bonds : bond 0.16346 ( 447) hydrogen bonds : angle 6.52391 ( 1223) covalent geometry : bond 0.00453 (11182) covalent geometry : angle 0.98970 (15600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.9085 (mt0) cc_final: 0.8484 (mm-40) REVERT: A 397 ASP cc_start: 0.7808 (t0) cc_final: 0.7533 (t0) REVERT: A 482 VAL cc_start: 0.9068 (t) cc_final: 0.8757 (p) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.2657 time to fit residues: 32.8054 Evaluate side-chains 76 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 511 HIS A 612 ASN A 754 HIS A1305 GLN A1349 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.092296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.068565 restraints weight = 41017.269| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.41 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11182 Z= 0.162 Angle : 0.607 10.630 15600 Z= 0.320 Chirality : 0.039 0.204 1820 Planarity : 0.004 0.043 1561 Dihedral : 19.731 155.596 2729 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.77 % Allowed : 17.63 % Favored : 79.60 % 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: -0.38 (0.25), residues: 1008 helix: 0.10 (0.23), residues: 509 sheet: -0.19 (0.55), residues: 96 loop : -0.54 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 18 HIS 0.007 0.001 HIS A 137 PHE 0.017 0.002 PHE A 966 TYR 0.020 0.002 TYR A 450 ARG 0.007 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 447) hydrogen bonds : angle 4.69733 ( 1223) covalent geometry : bond 0.00343 (11182) covalent geometry : angle 0.60685 (15600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8676 (tp) cc_final: 0.8467 (tp) REVERT: A 332 LEU cc_start: 0.9013 (tp) cc_final: 0.8809 (tt) REVERT: A 397 ASP cc_start: 0.8204 (t0) cc_final: 0.7948 (t0) REVERT: A 495 MET cc_start: 0.7663 (mmm) cc_final: 0.7455 (mmp) REVERT: A 961 LYS cc_start: 0.9277 (mttt) cc_final: 0.9040 (mppt) REVERT: A 1099 GLU cc_start: 0.8548 (pm20) cc_final: 0.8262 (pm20) REVERT: A 1108 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7428 (mp0) outliers start: 25 outliers final: 12 residues processed: 93 average time/residue: 0.3546 time to fit residues: 49.8025 Evaluate side-chains 76 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A1335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.088689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064922 restraints weight = 42413.080| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.45 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11182 Z= 0.169 Angle : 0.582 10.694 15600 Z= 0.310 Chirality : 0.038 0.201 1820 Planarity : 0.004 0.033 1561 Dihedral : 19.538 152.856 2727 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.10 % Allowed : 17.63 % Favored : 79.27 % 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: -0.26 (0.25), residues: 1008 helix: 0.34 (0.23), residues: 520 sheet: -0.03 (0.57), residues: 96 loop : -0.76 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1136 HIS 0.007 0.001 HIS A 137 PHE 0.018 0.002 PHE A1258 TYR 0.023 0.002 TYR A 988 ARG 0.006 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 447) hydrogen bonds : angle 4.49310 ( 1223) covalent geometry : bond 0.00359 (11182) covalent geometry : angle 0.58232 (15600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8576 (mmm) cc_final: 0.8338 (tpt) REVERT: A 397 ASP cc_start: 0.8473 (t0) cc_final: 0.8232 (t0) REVERT: A 510 LYS cc_start: 0.8418 (tptt) cc_final: 0.8213 (mptt) REVERT: A 650 GLN cc_start: 0.8476 (tt0) cc_final: 0.8204 (pt0) REVERT: A 961 LYS cc_start: 0.9268 (mttt) cc_final: 0.8984 (mppt) REVERT: A 1099 GLU cc_start: 0.8610 (pm20) cc_final: 0.8344 (pm20) REVERT: A 1150 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: A 1208 ASN cc_start: 0.9185 (t0) cc_final: 0.8896 (t0) REVERT: A 1276 PHE cc_start: 0.8875 (t80) cc_final: 0.8600 (t80) outliers start: 28 outliers final: 13 residues processed: 88 average time/residue: 0.2447 time to fit residues: 31.8542 Evaluate side-chains 73 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 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 = 0.4027 r_free = 0.4027 target = 0.088846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065061 restraints weight = 42116.145| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.47 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11182 Z= 0.138 Angle : 0.538 10.135 15600 Z= 0.282 Chirality : 0.037 0.196 1820 Planarity : 0.003 0.032 1561 Dihedral : 19.512 152.762 2727 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.99 % Allowed : 18.29 % Favored : 78.71 % 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: 0.06 (0.26), residues: 1008 helix: 0.66 (0.23), residues: 518 sheet: 0.08 (0.62), residues: 80 loop : -0.68 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.005 0.001 HIS A 137 PHE 0.015 0.001 PHE A 98 TYR 0.018 0.002 TYR A 450 ARG 0.004 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 447) hydrogen bonds : angle 4.23427 ( 1223) covalent geometry : bond 0.00294 (11182) covalent geometry : angle 0.53833 (15600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.134 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 58 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 130 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8620 (pp20) REVERT: A 196 PHE cc_start: 0.4964 (p90) cc_final: 0.4412 (p90) REVERT: A 395 ARG cc_start: 0.8972 (mtm110) cc_final: 0.8681 (ttm-80) REVERT: A 482 VAL cc_start: 0.8948 (t) cc_final: 0.8712 (p) REVERT: A 961 LYS cc_start: 0.9275 (mttt) cc_final: 0.8977 (mppt) REVERT: A 1099 GLU cc_start: 0.8600 (pm20) cc_final: 0.8301 (pm20) REVERT: A 1208 ASN cc_start: 0.9138 (t0) cc_final: 0.8788 (t0) REVERT: A 1276 PHE cc_start: 0.8917 (t80) cc_final: 0.8667 (t80) REVERT: A 1287 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8502 (mm) outliers start: 27 outliers final: 15 residues processed: 88 average time/residue: 0.2369 time to fit residues: 30.2478 Evaluate side-chains 80 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.090232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.066683 restraints weight = 41863.466| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.46 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11182 Z= 0.106 Angle : 0.508 9.702 15600 Z= 0.266 Chirality : 0.036 0.199 1820 Planarity : 0.003 0.032 1561 Dihedral : 19.362 150.718 2727 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.22 % Allowed : 18.63 % Favored : 78.16 % 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: 0.18 (0.26), residues: 1008 helix: 0.81 (0.23), residues: 520 sheet: 0.09 (0.61), residues: 80 loop : -0.68 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 137 PHE 0.028 0.001 PHE A 693 TYR 0.017 0.001 TYR A 136 ARG 0.007 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 447) hydrogen bonds : angle 4.09579 ( 1223) covalent geometry : bond 0.00223 (11182) covalent geometry : angle 0.50802 (15600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 130 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: A 196 PHE cc_start: 0.4827 (p90) cc_final: 0.4305 (p90) REVERT: A 395 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8669 (ttm-80) REVERT: A 482 VAL cc_start: 0.8998 (t) cc_final: 0.8791 (p) REVERT: A 510 LYS cc_start: 0.8542 (tptt) cc_final: 0.8181 (tppt) REVERT: A 961 LYS cc_start: 0.9266 (mttt) cc_final: 0.8958 (mppt) REVERT: A 1099 GLU cc_start: 0.8556 (pm20) cc_final: 0.8256 (pm20) REVERT: A 1208 ASN cc_start: 0.9112 (t0) cc_final: 0.8748 (t0) outliers start: 29 outliers final: 15 residues processed: 90 average time/residue: 0.2358 time to fit residues: 30.9656 Evaluate side-chains 80 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.087139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063651 restraints weight = 47115.968| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.36 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11182 Z= 0.290 Angle : 0.680 9.076 15600 Z= 0.360 Chirality : 0.042 0.206 1820 Planarity : 0.004 0.037 1561 Dihedral : 19.881 158.432 2727 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.77 % Allowed : 18.51 % Favored : 77.72 % 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: -0.26 (0.26), residues: 1008 helix: 0.44 (0.23), residues: 527 sheet: -0.31 (0.55), residues: 94 loop : -0.88 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1136 HIS 0.007 0.002 HIS A 328 PHE 0.021 0.002 PHE A 518 TYR 0.030 0.003 TYR A 450 ARG 0.006 0.001 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 447) hydrogen bonds : angle 4.68449 ( 1223) covalent geometry : bond 0.00609 (11182) covalent geometry : angle 0.68043 (15600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (pp20) REVERT: A 397 ASP cc_start: 0.8616 (t0) cc_final: 0.8228 (t0) REVERT: A 629 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7174 (mmp80) REVERT: A 734 LYS cc_start: 0.8623 (mttt) cc_final: 0.8275 (mttt) REVERT: A 958 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 961 LYS cc_start: 0.9310 (mttt) cc_final: 0.9016 (mppt) REVERT: A 1099 GLU cc_start: 0.8600 (pm20) cc_final: 0.8357 (pm20) outliers start: 34 outliers final: 24 residues processed: 88 average time/residue: 0.3784 time to fit residues: 46.7002 Evaluate side-chains 84 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 101 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 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 = 0.3975 r_free = 0.3975 target = 0.086448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062612 restraints weight = 43621.768| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.50 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11182 Z= 0.137 Angle : 0.538 9.451 15600 Z= 0.285 Chirality : 0.037 0.202 1820 Planarity : 0.003 0.033 1561 Dihedral : 19.537 152.386 2727 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.33 % Allowed : 19.73 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1008 helix: 0.78 (0.23), residues: 522 sheet: -0.19 (0.61), residues: 78 loop : -0.82 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.012 0.001 HIS A 511 PHE 0.015 0.001 PHE A 98 TYR 0.022 0.002 TYR A 136 ARG 0.003 0.000 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 447) hydrogen bonds : angle 4.30163 ( 1223) covalent geometry : bond 0.00294 (11182) covalent geometry : angle 0.53803 (15600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8817 (pp20) REVERT: A 395 ARG cc_start: 0.9063 (mtm110) cc_final: 0.8746 (ttm-80) REVERT: A 397 ASP cc_start: 0.8597 (t0) cc_final: 0.8388 (t0) REVERT: A 667 ILE cc_start: 0.9295 (mt) cc_final: 0.9057 (tp) REVERT: A 694 MET cc_start: 0.8544 (tpt) cc_final: 0.8342 (tpt) REVERT: A 734 LYS cc_start: 0.8600 (mttt) cc_final: 0.8209 (mttt) REVERT: A 958 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7760 (tp) REVERT: A 961 LYS cc_start: 0.9303 (mttt) cc_final: 0.9003 (mppt) REVERT: A 1099 GLU cc_start: 0.8594 (pm20) cc_final: 0.8343 (pm20) outliers start: 30 outliers final: 21 residues processed: 87 average time/residue: 0.3719 time to fit residues: 47.2334 Evaluate side-chains 81 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.086965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063754 restraints weight = 46946.828| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.29 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11182 Z= 0.241 Angle : 0.620 8.773 15600 Z= 0.330 Chirality : 0.040 0.201 1820 Planarity : 0.004 0.032 1561 Dihedral : 19.678 156.315 2727 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.22 % Allowed : 20.07 % Favored : 76.72 % 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: -0.18 (0.26), residues: 1008 helix: 0.59 (0.23), residues: 520 sheet: -0.27 (0.60), residues: 79 loop : -0.92 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.006 0.002 HIS A 328 PHE 0.037 0.002 PHE A 693 TYR 0.025 0.002 TYR A 136 ARG 0.003 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 447) hydrogen bonds : angle 4.56215 ( 1223) covalent geometry : bond 0.00511 (11182) covalent geometry : angle 0.61980 (15600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 2.029 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 60 GLU cc_start: 0.8681 (mp0) cc_final: 0.8469 (pm20) REVERT: A 130 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8923 (pp20) REVERT: A 395 ARG cc_start: 0.9101 (mtm110) cc_final: 0.8763 (ttm-80) REVERT: A 629 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7342 (mmp-170) REVERT: A 667 ILE cc_start: 0.9447 (mt) cc_final: 0.9206 (tp) REVERT: A 734 LYS cc_start: 0.8733 (mttt) cc_final: 0.8384 (mttt) REVERT: A 961 LYS cc_start: 0.9303 (mttt) cc_final: 0.9011 (mppt) REVERT: A 1099 GLU cc_start: 0.8561 (pm20) cc_final: 0.8328 (pm20) outliers start: 29 outliers final: 24 residues processed: 81 average time/residue: 0.3206 time to fit residues: 36.6350 Evaluate side-chains 83 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 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 = 0.3967 r_free = 0.3967 target = 0.087357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064307 restraints weight = 47200.793| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 4.30 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11182 Z= 0.201 Angle : 0.589 9.258 15600 Z= 0.313 Chirality : 0.039 0.315 1820 Planarity : 0.004 0.033 1561 Dihedral : 19.559 153.719 2727 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.10 % Allowed : 20.07 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1008 helix: 0.65 (0.23), residues: 523 sheet: -0.57 (0.59), residues: 83 loop : -1.03 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.039 0.002 PHE A 693 TYR 0.025 0.002 TYR A 136 ARG 0.003 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 447) hydrogen bonds : angle 4.49442 ( 1223) covalent geometry : bond 0.00429 (11182) covalent geometry : angle 0.58937 (15600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8655 (mp0) cc_final: 0.8412 (pm20) REVERT: A 130 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8974 (pp20) REVERT: A 395 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8723 (ttm-80) REVERT: A 629 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7339 (mmp-170) REVERT: A 667 ILE cc_start: 0.9430 (mt) cc_final: 0.9186 (tp) REVERT: A 734 LYS cc_start: 0.8827 (mttt) cc_final: 0.8459 (mttt) REVERT: A 961 LYS cc_start: 0.9302 (mttt) cc_final: 0.8996 (mppt) REVERT: A 1099 GLU cc_start: 0.8564 (pm20) cc_final: 0.8328 (pm20) outliers start: 28 outliers final: 26 residues processed: 83 average time/residue: 0.3992 time to fit residues: 48.4605 Evaluate side-chains 84 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 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 = 0.3974 r_free = 0.3974 target = 0.086178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.063185 restraints weight = 42316.642| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.31 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11182 Z= 0.118 Angle : 0.540 10.264 15600 Z= 0.284 Chirality : 0.037 0.315 1820 Planarity : 0.003 0.034 1561 Dihedral : 19.276 150.720 2727 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.88 % Allowed : 20.51 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1008 helix: 0.91 (0.24), residues: 523 sheet: -0.48 (0.59), residues: 83 loop : -0.84 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 137 PHE 0.055 0.002 PHE A 693 TYR 0.022 0.002 TYR A1326 ARG 0.003 0.000 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 447) hydrogen bonds : angle 4.26633 ( 1223) covalent geometry : bond 0.00251 (11182) covalent geometry : angle 0.53993 (15600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 2.444 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 60 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: A 130 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8957 (pp20) REVERT: A 395 ARG cc_start: 0.9064 (mtm110) cc_final: 0.8730 (ttm-80) REVERT: A 482 VAL cc_start: 0.8863 (t) cc_final: 0.8593 (p) REVERT: A 667 ILE cc_start: 0.9326 (mt) cc_final: 0.9059 (tp) REVERT: A 734 LYS cc_start: 0.8796 (mttt) cc_final: 0.8412 (mttt) REVERT: A 961 LYS cc_start: 0.9299 (mttt) cc_final: 0.8982 (mppt) REVERT: A 1099 GLU cc_start: 0.8576 (pm20) cc_final: 0.8324 (pm20) outliers start: 26 outliers final: 22 residues processed: 86 average time/residue: 0.3354 time to fit residues: 41.3222 Evaluate side-chains 90 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 57 optimal weight: 0.0370 chunk 88 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 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 = 0.3942 r_free = 0.3942 target = 0.084610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.061116 restraints weight = 42814.849| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.19 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11182 Z= 0.167 Angle : 0.572 10.652 15600 Z= 0.302 Chirality : 0.038 0.311 1820 Planarity : 0.004 0.033 1561 Dihedral : 19.361 153.604 2727 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.66 % Allowed : 21.18 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1008 helix: 0.85 (0.23), residues: 523 sheet: -0.45 (0.59), residues: 84 loop : -0.95 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.008 0.001 HIS A 511 PHE 0.044 0.002 PHE A 693 TYR 0.023 0.002 TYR A 136 ARG 0.003 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 447) hydrogen bonds : angle 4.35180 ( 1223) covalent geometry : bond 0.00359 (11182) covalent geometry : angle 0.57191 (15600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.62 seconds wall clock time: 109 minutes 35.82 seconds (6575.82 seconds total)